I have the exact same problem (running very latest debian unstable,
problems commencing with last massive xorg change) with emacs starting
up and displaying only boxes where the text should be... and also
displaying these 2 messages on the command line at startup:

Warning: Cannot convert string 
"-*-courier-medium-r-*-*-*-120-*-*-*-*-iso8859-*" to type FontStruct
Warning: Cannot convert string 
"-*-helvetica-medium-r-*--*-120-*-*-*-*-iso8859-1" to type FontStruct

I was able to restore emacs to a usable state by loading certain fonts
(detailed below).  Initially, i troubleshot the problem by going into
"Options', "Mule", "Set Font/Fontset", "Fontset", "standard: 16-dot medium"
This was the only item under Fontset that would display text properly.

Doing this immediately after startup with the red & blue emacs logo
still being displayed does cause a segfault but otherwise (once the logo
is gone) works ok.

Font details:

Most of the adobe fonts don't work, except for adobe-courier, for ex:

(set-frame-font "-adobe-courier-medium-r-normal--14-140-75-75-m-90-iso8859-1") 
works

Non-working adobe fonts include (all the rest):
  -adobe-helvetica-
  -adobe-new century schoolbook-
  -adobe-symbol-
  -adobe-times-
  -adobe-utopia-

With these, everything shows as boxes (seemingly of the correct
size)... except for the adobe-utopia fonts which don't seem to be found
at all (on my system)... `set-frame-font' with any of these gives a
backtrace saying the font isn't defined.)

The rest of the fonts mostly work:

-b&h-lucida-
-b&h-lucidabright-
-b&h-lucidatypewriter-
-bitstream-charter-
-misc-fixed-
6x10, 10x20, 12x24, ...
lucidasans-

with the following peculiar exceptions:

(set-frame-font 
"-b&h-lucidabright-demibold-r-normal--19-190-75-75-p-114-iso10646-1")
(set-frame-font 
"-b&h-lucidabright-demibold-r-normal--20-140-100-100-p-118-iso8859-1")

(set-frame-font "kanji24")   works
(set-frame-font "kanji16")   doesn't

(set-frame-font "olglyph-10")   works
(set-frame-font "olglyph-12")   works
(set-frame-font "olglyph-14")   works
(set-frame-font "olglyph-19")   doesn't

(set-frame-font 
"-jis-fixed-medium-r-normal--24-170-100-100-c-240-jisx0208.1983-0")  works
(set-frame-font 
"-jis-fixed-medium-r-normal--16-110-100-100-c-160-jisx0208.1983-0")  doesn't

There was also an intermittent problem when changing from one font to
another.  Every once in a while changing to a working font would display
all boxes as if that font didn't work.  It was pretty much a random
thing.  Once i got back to a working font, changing to the font that
messed things up on the previous switch would then work ok.  Once things
got messed up due to this random glitch, changing to another working
font generally did not fix the problem, i.e. the new font also displayed
as boxes.  There was one font that _always_ displayed properly which i
came to rely upon to get things back to normal whenever this glitch
occurred: "-adobe-courier-medium-r-normal--12-120-75-75-m-70-iso8859-1"


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