Ok, I was able to fix everything the way I had wanted.
I looked at some of the comments made for this bug 
(https://bugs.launchpad.net/ubuntu/+bug/219931)

There, someone mentions that:
>it's not the fonts which cause these issues, it's the fontconfig configuration 
>on your system, which prefers certain fonts over others in specific 
>situations. As the ja_JP setting in fontconfig-voodoo is optimized for 
>Japanese users who do not use extended Latin characters, this is indeed 
>expected behavior. If you prefer DejaVu or any other font fir Latin script, I 
>suggest that you copy /etc/fonts/conf.avail/69-language-selector-ja-jp.conf to 
>~/.fonts.conf, then edit this file and add the DejaVu or other font entries at 
>the top of each font list for serif, sans-serif and monospace. This should fix 
>your problem.

So I created ~/.fonts.conf by copying 69-language-selector-ja-jp.conf.
I then added DejaVu fonts into fonts.conf as the first font setting for all 
three sections in the file, and I also added the following code (taken from 
above):
<fontconfig>
 <match target="font">
  <test name="lang" compare="contains">
   <string>ja</string>
  </test>
  <edit name="embeddedbitmap" mode="assign">
   <bool>false</bool>
  </edit>
  <edit name="autohint" mode="assign">
   <bool>true</bool>
  </edit>
  <edit name="antialias" mode="assign">
   <bool>true</bool>
  </edit>
  <edit name="hintstyle" mode="assign">
   <const>hintnone</const>
  </edit>
 </match>
</fontconfig>

I attached my .fonts.conf which maintains the good Latin characters as
well as Japanese characters (both fonts are smoothed and anti-aliased).

** Attachment added: ".fonts.conf"
   http://launchpadlibrarian.net/34027457/fonts.txt

-- 
Without ja_JP as default environment, Japanese font looks horrible for certain 
font sizes
https://bugs.launchpad.net/bugs/36761
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