If I am repeating things you have already tried, my apologies, but FWIW….
You often accumulate fonts without knowing about it because they get installed by third party applications without notification. Your reinstall should have cleaned up the system Font Library (/System/Library/Fonts) and as a system owned folder it is not supposed to be modified by Migration Assistant. However just to be sure, you will find a list of the standard Snow Leopard fonts and what folder they should be in
here. There should be nothing in /System/Library/Fonts (the system font library) other than the listed
system fonts.
The freeware app
TinkerTool will show you what system fonts (typeface and size) are in use and will allow you to either change them to suit your personal preference, or set them back to the default. You might see if you can "fix" your problem by changing fonts. By-the-way although you do not want to add or delete fonts in /System/Library/Fonts you can assign fonts not in that folder to system tasks. For Example I use Lucida Bright for applications, and Lucida Sans as the system fixed pitch font.
MIgration Assistant may have modified the contents of /Library/Fonts and definitely would have modified ~/Library/Fonts in your user home folder. The encodings.dir, fonts.dir, fonts.list, fonts.scale are expected in the /Library/Fonts which contain the fonts available to any user. You may also have some font files in ~/Library/Fonts in your user home folder but
you should not have duplicated fonts between the three different font libraries. There is a Font Book option to search for duplicate activated fonts. (Font Book > Edit > Look for enabled duplicates…).
The ProKit update you installed does effect font smoothing so it was certainly well worth installing. Speaking of font smoothing, you may have already mentioned it, but have you tried adjusting the font smoothing settings in System Preferences > General?
