So I recently upgraded my Morrowind Overhaul from 2 to 3. As you know it requires a re-install of everything which is exactly as I did. I also downloaded the official plug ins after the main install and the overhaul was done. I continued from one of my previous save files and got messages that said some meshes could not be found. Underestimating the problem I went into the game. While I admit this isn't a game breaking issue, when I enter certain areas such as the Legion outpost in Gnisis I get messages telling me there is missing meshes and if I wanted to continue loading. If I press ok one of the tables in the room is gone and in it's place is a yellow light. This is just one example of the problem I've found several more in Vivec though I can't seem to recall where specifically.

I really do not wish to start a new game over again, and given the possibility that the problem might even persist with that, I was wondering if anyone knows a fix for these mesh errors.

Check the first post of this thread: http://www.gamesas.com/topic/1446220-relz-morrowind-overhaul-sounds-graphics-30-by-kingpix-thread-3/

Look for John.Moonsugar's Unofficial Patch. I don't use MGSO myself but that should fix things for you. If not, post in that thread: the people who know the compilation better than I will more likely see your problem there.

[Edit: typo]