LOL happy accidental discovery...
So, in the process of moving exes and update.rpf around I forgot to put vanilla update.rpf back into the main update folder. Funny that that the game still ran without it. My thought it because the game was using the copy on the mods folder instead of the vanilla file. I'm going to experiment with this new discovery and see what happens.
Ok so, moving the files to mods folder (keeping a backup on a separate drive to save time and not have to redownload files if something broke) works...sort of. Update/X64 needs to be in the main game folder or Sociial Club won't initialize. Everything file I planned to mod moved. Game started almost normally. Loaded slow and there was a message "Loading Model" in the lower right corner. Game crashed before loading finished. This with unmodded vanilla files.