I have several mods that change the Menu.ini and the Commands.cfg. I long ago got into the habit of comparing both files with every mod I wanted to install. Once I had it set up exactly the way I wanted I would make a copy of the final version of each. If I had to reinstall everything I would just add all the relevant visual files and then put a copy of the two big files back into the game.
Earlier I tore out the whole version I was working on and used Multi-SH3 to start over. Rather than add any mods I played the 'Happy Times' single mission. It's been a long time since I've actually attacked anything, and it was fun.
