It is a button difficult to resist at times... "Verify Integrity"... sounds good, but yeah, it will mess things up in a modded game. What I did with my Steam install, was I made a copy of my game directory, and pasted it into a new folder, and that is the copy that I mod. I leave the original install alone (you can verify it without worry). You can add the "new" game executable to the Steam start menu (which of course has that "Verify file integrity" button on it), and rename it something appropriate. I also use MultiSH4 v1.5 and create a new save folder for the modded version.
