I recently tried installing the latest version of MGSO. I did a clean reinstall of Morrowind, the patches, and the expansions, and ran the MGSO program. After all of it finished up, I booted up Morrowind, and it failed to load; it said something about "font 0 missing". I figured it was an error in Morrowind.ini, so I went in and, sure enough, there were no lines for font. I copied them from the vanilla Morrowind.ini I had, and, sure enough, it managed to make it to the main menu of Morrowind without problem. When I tried to start a game, however, the screen turned black, and Morrowind stopped responding. After looking through Morrowind.ini more thoroughly, I noticed that it was missing a lot of lines, probably well over half. Any help is as to why this is and what I can do to fix it would be greatly appreciated.

Try running the game again and make a note of exactly what the warning messages say, Also in your Morrowind folder there is a text document named 'Warnings' if you could copy and paste the contents here that should provide important clues as to what is wrong.

If you did not run Morrowind once before installing, that may be why the .ini file was missing lines.