Ossie Wilson wrote:
I have attached the Ly file

After a cursory look, I would say this file is badly mangled as regards key signatures. In part one at bar 29 it helps to say \key df instead of \key cs because the subseqent notes are e.g. df, gf, ...

Also part one should declare _at_least_ one additional key change: at bar 13, to \key gf \major This is odd because to insert this in the "low" voices you have to first split up the initial 26 silent bars. But then again, at the top it says "Generated from a MIDI File by LyFromMIDI ..."

So \transpose isn't really your problem at the moment. You have to get it looking right in the original first.
Cheers,
Robin

P.S. And yes, Win98 users are stuck at 2.8. 
\version "2.8.6"
\paper {
    #(set-paper-size "a4")
    line-width = 20\cm
    print-page-number =##t
    printfirst-page-number = ##t
    between-system-space = 0.1 \cm
    after-title-space = 0.1 \cm
    ragged-bottom =##f
    ragged-first-bottom = ##f
    top-margin = 0.16 \cm
    head-separation = 0.04 \cm
    bottom-margin = 0.1 \cm
    left-margin = 0.4 \cm
}
	
#(set-global-staff-size 18)
\include "english.ly"

\header {
   composer =  "Richard Rodgers"
   poet = "Oscar Hammerstein II"
   copyright = ""   %"Copyright © 2006 by O.A.Wilson"
   title = "If I Loved You"
   subtitle = ""
   tagline =""   % "Generated from a MIDI File by LyFromMIDI and then Typeset by LilyPond"
}


melodyone =   {
     \time  2/4
     \key g \major
     \clef treble             
     \stemNeutral  

% Bar  1 
     \tempo 4 = 104
     R1*2/4 
% Bar  2 
     R1*2/4     
% Bar  3
     R1*2/4      
% Bar  4
      r4 d'8 d'  \break   
% Bar  5
      g'4 g'8 g'   
% Bar  6
     g'2     
% Bar  7
     g'8 d' g' a'    
% Bar  8
     g'4 r8 d'8  \break    
% Bar  9
     g'4 g'8 g'    
% Bar  10
     g'8. d'16 g'8 a'
% Bar  11
     g'2 ~
% Bar  12
     g'4 r8 g'8  \break
% Bar  13
     \key gf \major
     gf'8. gf'16 gf'8 gf'
% Bar  14
     gf'8 gf'4 gf'8
% Bar  15
     gf'8. gf'16 gf'8 gf'
% Bar  16
     gf'8 r8 gf'8 gf'   \break
% Bar  17
     gf'4. gf'8
% Bar  18
     gf'4 gf'8 gf'
% Bar  19
     gf'2 ~   \break
% Bar  20
     gf'8 \breathe r8 gf'8^\markup {\italic  {meno mosso } } gf'
% Bar  21
     bf'2
% Bar  22
     bf'2 ~
% Bar  23
     bf'2 ~  \break
% Bar  24
     bf'4^\fermata \breathe r8 bf'8
% Bar  25
     bf'8.^\markup {\italic { poco rit. }}  ef'16 ef'8 ef'
% Bar  26
     ef'4. ef'16 ef'
% Bar  27
     f'8 af' df' f'   \break
% Bar  28
     c'2^\fermata \bar "||" 
% Bar  29
     \key df \major
     \time 4/4 
     df'2^\markup {\italic "a tempo (" \smaller \note #"4" #1 " = 82)"} f'
% Bar  30
     bf'4 bf'2.  \break
% Bar  31
     df''4 ~ \times 2/3 {df''8 c'' bf'} af'4 ~ \times 2/3 {af'8 gf' f' } 
% Bar  32
     ef'4 df' f'2
% Bar  33
     ef'2 gf'  \break
% Bar  34
     c''4 c''2 df''4
% Bar  35
     af'1 ~
% Bar  36
      af'2. r4 \break
% Bar  37
     df'2^\markup {\italic "piu mosso" } f'
% Bar  38
     bf'4 bf'2.
% Bar  39
     df''4 ~ \times 2/3 {df''8 c'' bf'} af'4 ~ \times 2/3 {af'8 gf' f'} \break
% Bar  40
     ef'4 df' f'2     
% Bar  41
     ef'2 gf'
% Bar  42
     c''4 c''2 df''4  \break
% Bar  43
     df''1 ~
% Bar  44
     df''2 ~ df''4 r4  \mark \markup { \musicglyph #"scripts.segno" } 
% Bar  45
     \bar "||" df''2 c''4 bf'  \break
% Bar  46
     af'4 gf' r4 af'8 bf'
% Bar  47
     c''2 c''
% Bar  48
     c''2 ~ c''4. r8  \break
% Bar  49
     df''2 c''4 bf'
% Bar  50
     af'4 gf' af' bf'
% Bar  51
     ef''2 ef''  \break
% Bar  52
     ef''2 ~ ef''4. r8
% Bar  53
     df''2 f'
% Bar  54
     bf'4 bf'2.  \break
% Bar  55
     df''4 ~  \times 2/3 {df''8 c'' bf'} af'4 ~ \times 2/3 {af'8 gf' f' } 
% Bar  56
     ef'4 df' f'2
% Bar  57
     ef'2 gf'  \break
% Bar  58
     c''4 c''2 df''4^\markup { \hspace #3.4 "to      CODA" }  \mark \markup { \musicglyph #"scripts.coda" } 
% Bar  59
     f''1 ~
% Bar  60
     f''2. r4  \break
% Bar  61
     ef''2 f''
% Bar  62
     gf''4 gf''2. ~
% Bar  63
     gf''2. r4  \break
% Bar  64
     bf'2^\markup { \italic rit. } c''
% Bar  65
     df''4 df''2. ~
% Bar  66
     df''2 r2^\markup { \hspace #-4.5 {\large \bold {"D.S. al  " \raise #1 \musicglyph #"scripts.coda"  " CODA" }}}  \bar "||"  \break
}

% End of Notes

melodytwo =   {
     \time  4/4
     \key df \major
     \clef treble             
     \stemNeutral 
        
% Bar  67
     \set Score.currentBarNumber = #67
     f''1^\markup { \hspace #'-4 \raise #2 { \large \bold \musicglyph #"scripts.coda" \raise #-1 " CODA" } }  ~    
% Bar  68
     f''2. r4    
% Bar  69
     ef''2 f''2  \break
% Bar  70
     gf''4 gf''2. ~ 
% Bar  71
     gf''2. r4
% Bar  72
     bf'2^\markup { \italic "rit." }  c''
% Bar  73
     df''1^\markup { \italic "a tempo" }       \break
% Bar  74
     df''1 ~
% Bar  75
     df''1 ~ 
% Bar  76
     df''2. r4 \breathe
% Bar  77
     R1^\fermataMarkup  \break
% Bar  78       
         
     \bar "|."
}


textone = \lyricmode {
 When I worked in the mill, weav -- ing at the loom, I'd gaze ab -- sent mind -- ed at the roof' and half the time the shut -- tle would tan -- gle in the threads, and the warp get mixed with the woof. If I loved you! But some -- how I can see just ex -- act -- ly how I'd be If I loved you. time and a -- gain I would try to say all I'd want you to know. If I loved you, words would -- n't come in an eas -- y way' round in cir -- cles I'd go. Long -- ing to tell you, but a -- fraid and shy, I'd let my gold -- en chanc -- es pass me by Soon you'd leave me, off you would go in the mist of day, nev -- er nev -- er to know how I loved you, if I loved you.  
}

texttwo = \lyricmode {
   know how I loved you, if I loved you.
}


rightone =  {
     \time  2/4
     \key g  \major
     \clef treble   
     \stemUp
     \slurUp
     \tieUp
     \phrasingSlurUp

% Start of Notes

 % Bar  1 
     \stemDown <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)
% Bar  2 
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''> \)    
% Bar  3
     <b' g''>8 \(<c'' a''> < d'' b''> <c'' a''>\)      
% Bar  4
     <b' g''>8 \(<c'' a''> < d'' b''> <c'' a''>\)         
% Bar  5
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)         
% Bar  6
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)         
% Bar  7
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)         
% Bar  8
     <b' g''>8 \(<c'' a''> < d'' b''> <c'' a''>\)         
% Bar  9
     <b' g''>8\(<c'' a''> < d'' b''> <c'' a''>\)         
% Bar  10
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)
% Bar  11
     <b' g''>8 \(<c'' a''> < d'' b''> <c'' a''>\)
% Bar  12
     <b' g''>8\( <c'' a''> < d'' b''> <c'' a''>\)
% Bar  13
     \key gf \major
     <bf' gf''>8\( <cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  14
     <bf' gf''>8\(<cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  15
     <bf' gf''>8\( <cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  16
     <bf' gf''>8\( <cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  17
     <bf' gf''>8\(<cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  18
     <bf' gf''>8\( <cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  19
     <bf' gf''>8\( <cf'' af''> <df'' bf''> <cf'' af''>\)
% Bar  20
     <bf' gf''>8 \breathe r8 r4 \stemUp
% Bar  21
     d'8 \( ef' f' ef'\)
% Bar  22
     d'2 ~
% Bar  23
     d'2 ~
% Bar  24
     d'4^\fermata \breathe r4
% Bar  25
     <bf ef' bf'>2 ~ 
% Bar  26
     <bf ef' bf'>2
% Bar  27
     <af af'>2
% Bar  28
     f'4  ef'^\fermata  \bar "||"
% Bar  29
     \key df \major
     \time 4/4
     r8 f'4. r8 f'4.
% Bar  30
     r8 g'4. r8 g'4. 
% Bar  31
     r8 f'4. r8 f'4. 
% Bar  32
     r8 f'4. r8 f'4.
% Bar  33
     r8 gf'4. r8 gf'4.
% Bar  34
     r8 bf'4. r8 bf'4.
% Bar  35
     r8 f'4. r8 f'4.
% Bar  36
     r8 f'4. r8 f'4.
% Bar  37
     r8 f'4. r8 f'4.
% Bar  38
     r8 g'4. r8 g'4.
% Bar  39
     r8 f'4. r8 f'4.
% Bar  40
     r8 f'4. r8 f'4.     
% Bar  41
     r8 gf'4. r8 gf'4.
% Bar  42
     r8 bf'4. r8 bf'4.
% Bar  43
     af'1
% Bar  44
     a'4 ~ a'8 bf'16 c'' df''4 c'' \bar "||"
% Bar  45
     df''2 c''4 bf'
% Bar  46
     af'4 gf' af' bf'
% Bar  47
     c''2 c''
% Bar  48
     c''1
% Bar  49
     df''2 c''4bf'
% Bar  50
     af'4 gf' af' bf'
% Bar  51
     ef''2 ef''
% Bar  52
     ef''1
% Bar  53
     r8 f'4. r8 f'4.
% Bar  54
     r8 gf'4. r8 g'4.
% Bar  55
     r8 f'4. r8 f'4.
% Bar  56
     r8 f'4. r8 f'4.
% Bar  57
     r8 gf'4. r8 gf'4.
% Bar  58
     r8 bf'4. r8 bf'4.
% Bar  59
     df''2( c'')
% Bar  60
     df''2( c'')
% Bar  61
     ef''2 f''
% Bar  62
     gf''4 gf''2. 
% Bar  63
     R1
% Bar  64
     <df' f' gf' bf'>2 <ef' gf' af' c''>
% Bar  65
     <af' df'' >1
% Bar  66
     af'2 a'4\( bf'8 c''\) \bar "||"
    
}

rightonelow =  {
     \time  2/4
     \key g  \major
     \clef treble   
     \stemDown
     \tieDown
     \slurDown
     \phrasingSlurDown

% Start of Notes

% Bar  1 
     s2*12 
% Bar  13
    \key gf \major
     s2*14 

% Bar  27
      ef'4( df')
% Bar  28
     <af c'>2  \bar "||"
% Bar  29
     \key df \major
     \time 4/4
     s8 af8\( df' af \) s8 af8\( df' af\)
% Bar  30
     s8 bf8\( e' g\) s8 bf \(e' g\)
% Bar  31
      s8 af8\( df' af\) s8 af\( df' af\)
% Bar  32
      s8 a8\( df' a\) s8 a\( df' a\)
% Bar  33
     s8 bf8 \(ef' bf\) s8 bf\( ef' bf\)
% Bar  34
     s8 c'8\( g' df'\) s8 c'\( g' df'\)
% Bar  35
     s8 af8\( df' af\) s8 af\( df' af\)
% Bar  36
      s8 af8 \(c' af\) s8 af\( c' af\)
% Bar  37
     s8 af8 \(df' af\) s8 af\( df' af\)
% Bar  38
     s8 bf8\( e' g\) s8 bf\( e' g\)
% Bar  39
      s8 af8\( df' af\) s8 af\( df' af\)
% Bar  40
     s8 a8\( df' a\) s8 a\( df' a\)     
% Bar  41
     s8 bf8\( ef' bf\) s8 bf\( ef' bf\)
% Bar  42
     s8 c'8\( g' df'\) s8 c'\( g' df'\)
% Bar  43
     r8 df'8\( f' df'\) r8 df'\( f' df'\)
% Bar  44
     r8 df'8\( f' df'\) r8 f' \(a' f'\)
% Bar  45
      r8 df'8\( f' df'\) r8 df'\( f' df'\)
% Bar  46
     r8 bf8\( ef' bf \) r8 bf \( ef' bf\)
% Bar  47
     r8 d'8\( fs' d' \) r8 d'\( fs' d' \)
% Bar  48
     r8 d'8\( fs' d'\) r8 d'\( fs' d'\)
% Bar  49
     r8 df'8\( f' df'\) r8 df'\( f' df'\)
% Bar  50
     r8 bf8\( ef' bf\) r8 bf \(ef' bf\)
% Bar  51
     r8 ef'8\( <gf' cf''> ef'\) r8 ef'\( <g' bf' df''> ef'\)
% Bar  52
     r8 ef'8\( <af' c''> ef'\) r8 ef'\( <gf' af' c''> ef'\)
% Bar  53
     s8 af8\( df' af \) s8 af \( df' af \)
% Bar  54
     s8 bf8\( e' g\) s8 bf \(e' g\)
% Bar  55
     s8 af8\( df' af\) s8 af\( df' af\)
% Bar  56
     s8 a8\( df' a\) s8 a\( df' a\)
% Bar  57
     s8 bf8\( ef' bf\) s8 bf\( ef' bf\)
% Bar  58
     s8 c'8\( g' df'\) s8 c'\( g' df'\)
% Bar  59
     r8 df'8\( <f' af'> df'\) r8 c'\( <f' af'> c'\)
% Bar  60
     r8 df'8\( <f' af'> df'\) r8 c' \(<f' af'> c'\)
% Bar  61
     r8 ef'8\( <gf' bf'> ef'\) r8 f'\( <af' df''> f'\)
% Bar  62
     r8 gf'8\( <bf' df'' ef''> gf'\) ~ <gf' bf' df'' ef''>2
% Bar  63
     R1
% Bar  64
     s1
% Bar  65
     f'2 c'4( f')
% Bar  66
     <df' f'>1 \bar "||"
    

}

% End of Notes

leftone =  {
     \time  2/4
     \key g  \major
     \clef bass 
     \stemUp
     \tieUp
     \slurUp
     \phrasingSlurUp

% Start of Notes

% Bar  1 
     \stemDown b8\( d' g' d'\)
% Bar  2 
     \stemDown b8\( d' g' d'\)     
% Bar  3
     \stemDown b8\( d' g' d'\)      
% Bar  4
     \stemDown b8\( d' g' d'\)         
% Bar  5
     \stemDown b8\( d' g' d'\)         
% Bar  6
     \stemDown b8\( d' g' d'\)         
% Bar  7
     \stemDown b8\( d' g' d'\)         
% Bar  8
     \stemDown b8\( d' g' d'\)         
% Bar  9
     \stemDown b8\( d' g' d'\)         
% Bar  10
     \stemDown b8\( d' g' d'\)
% Bar  11
     \stemDown b8\( d' g' d'\)
% Bar  12
     \stemDown b8\( d' g' d'\)
% Bar  13
    \key gf \major
     bf8 \( df' ef' df'\)
% Bar  14
     bf8\( df' ef' df'\)
% Bar  15
     bf8\( df' ef' df'\)
% Bar  16
     bf8\( df' ef' df'\)
% Bar  17
     bf8 \( df' ef' df'\)
% Bar  18
     bf8\( df' ef' df'\)
% Bar  19
     bf8\( df' ef' df'\)
% Bar  20
     bf8 \breathe r8 r4
% Bar  21
     f8 \(g af g
% Bar  22
     f8\) bf\( f d\)
% Bar  23
     \stemUp bf,2 ~
% Bar  24
     bf,4^\fermata \breathe r4
% Bar  25
     g,2 ~ 
% Bar  26
     g,2
% Bar  27
     f2
% Bar  28
     gf2 \bar "||"
% Bar  29
     \key df \major
    \time 4/4
     df2( df,)
% Bar  30
     df2(  df,)
% Bar  31
     f,2(  f)
% Bar  32
     f,2 ( f)
% Bar  33
     gf,2 (gf)
% Bar  34
     e,2 (e)
% Bar  35
     f,2( f)
% Bar  36
     f,2(  f)
% Bar  37
     df2 ( df,)
% Bar  38
     df2 ( df,)
% Bar  39
     f,2(  f)
% Bar  40
     f,2( f )    
% Bar  41
     gf,2( gf)
% Bar  42
     e,2( e)
% Bar  43
     f,2( f)
% Bar  44
     f,2( f)  \bar "||"
% Bar  45
     bf,2 bf,
% Bar  46
     ef,2 (ef)
% Bar  47
     d,2( d)
% Bar  48
     d,2( d)
% Bar  49
     df,2( df)
% Bar  50
     gf,2( gf)
% Bar  51
     cf2 bf,
% Bar  52
     af,2( af)
% Bar  53
     df2( df,)
% Bar  54
     df2( df,)
% Bar  55
     f,2( f)
% Bar  56
     f,2( f)
% Bar  57
     gf,2( gf)
% Bar  58
     e,2 (e)
% Bar  59
     af,2( f,)
% Bar  60
     af,2( f,)
% Bar  61
     <gf, gf>2 <f, f>
% Bar  62
     <ef, ef>4 <ef, ef>2.
% Bar  63
      R1
% Bar  64
     gf2 gf
% Bar  65
     df1 ~
% Bar  66
     df1

    
}


leftonelow =  {
     \time  2/4
     \key g \major
     \clef bass 
     \stemDown
     \tieDown
     \slurDown
     \phrasingSlurDown

% Start of Notes

% Bar  1 
     s2*12 
% Bar  13
    \key gf \major
     s2*14 

% Bar  27
     af,2 ~
% Bar  28
     af,2 \bar "||"
% Bar  29
     \key df \major
     \time 4/4
% Bar  30



}

% End of Notes

righttwo =  {
     \time  4/4
     \key df  \major
     \clef treble   
     \stemUp
     \tieUp
     \slurUp
     \phrasingSlurUp

% Start of Notes


% Bar  67
     <df'' f''>1 ~     
% Bar  68
     <df'' f''>1    
% Bar  69
     ef''2 f''
% Bar  70
     gf''4 gf''2.      
% Bar  71
     R1
% Bar  72
     <df' ef' gf' bf'>2\arpeggio <ef' gf' af' c''>\arpeggio
% Bar  73
     #(set-octavation 1)
     \set Staff.ottavation = #"8va"
     <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\)  
% Bar  74
     <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) 
% Bar  75
      <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) 
% Bar  76
     <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) <f'' df'''>8\( <gf'' ef'''> <af'' f'''> <gf'' ef'''>\) 
     #(set-octavation 0) \breathe
% Bar  77
     <f af df'>1\arpeggio^\fermata
% Bar  78
 
         
        \bar "|."
}

righttwolow =  {
     \time  4/4
     \key df  \major
     \clef treble   
     \stemDown
     \slurDown
     \phrasingSlurDown
     \tieDown

% Start of Notes
       
% Bar  67
     <f' af'>4 f'\( af' f' ~        
% Bar  68
     f'4\) f'\( af' f' \)   
% Bar  69
     r8 ef'8 \(<gf' bf'> ef'\) r8 f'\( <af' df''> f'\)
% Bar  70
     r8 gf'8\( <bf' df'' ef''> gf' \) ~ <gf' bf' df'' ef''>2 
% Bar  71
     s1
% Bar  72
     s1
% Bar  73
     s1 
 
         

}

lefttwo =  {
     \time  4/4
     \key df  \major
     \clef bass 
     \stemUp

% Start of Notes

% Bar  67
     <df, df>1    
% Bar  68
     <f, f>1    
% Bar  69
     <gf, gf>2 <f, f>
% Bar  70
     <ef, ef>4 <ef, ef>2. 
% Bar  71
     R1
% Bar  72
     gf2\arpeggio af\arpeggio
% Bar  73
     df1   \clef treble 
% Bar  74
     df'2 f'
% Bar  75
     bf'1 ~ 
% Bar  76
     bf'1  \clef bass \breathe
% Bar  77
     <df, df>1\arpeggio^\fermata
% Bar  78
 
         
         
        \bar "|."
}

lefttwolow =  {
     \time  4/4
     \key df \major
     \clef bass 
      \stemDown 

% Start of Notes
      
% Bar  67
     s1*11    
% Bar  68          

}

% End of Notes


\score {
<< 
   \new Voice =  "melone" {
   \autoBeamOff
  %{ \transpose g g %} 
 { \melodyone }
  }
  \new Lyrics \lyricsto melone \textone
  \new PianoStaff <<
    \set PianoStaff.connectArpeggios = ##t
	\new Staff = "treble" <<
	 \new Voice = "voice1" {   %{ \transpose g g %}   {\rightone }}
	 \new Voice = "voice2" {  %{ \transpose g g %}     {\rightonelow }}
	>>
	\new Staff = "bass" <<
	 \new Voice = "voice1" {   %{ \transpose g g %}    {\leftone }}
	 \new Voice = "voice2" {    %{ \transpose g g %}  {\leftonelow }}
	>>
 	>>
>>
\layout  { 
      indent = 2.0 \cm
       linewidth = 18.0 \cm
     interscoreline = 0.2 \cm 
 }
      \midi {}

} 

\score {
 << 
   \new Voice =  "meltwo" {
   \autoBeamOff
  \transpose g ds 

 { \melodytwo }
  }
  \new Lyrics \lyricsto meltwo  \texttwo
  \new PianoStaff <<
    \set PianoStaff.connectArpeggios = ##t
	\new Staff = "treble" <<
	 \new Voice = "voice1" {   \transpose g ds    {\righttwo }}
	 \new Voice = "voice2" {  \transpose g ds   { \righttwolow }}
	>>
	\new Staff = "bass" <<
	 \new Voice = "voice1" {   \transpose g ds    { \lefttwo }}
	 \new Voice = "voice2" {   \transpose g ds    { \lefttwolow }}
	>>
 	>>
 >>
\layout  { 
      indent = 2.0 \cm
       linewidth = 18.0 \cm
     interscoreline = 0.2 \cm 
      }
 }


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