Honestly, you are better off with a new install of the game. The main issue is the Save folder (the "C:\User \UserName \Documents \SH4" folder). The way the game Saves files is somewhat unconventional (possibly for modding??), and holds all sorts of info about all aspects of the game install and your play. One little mistaken cross-touch of an obsolete file from the Save folder into the game, and "Boom!", CTD and / or corrupted Save.
Once you wrap your head around JSGME (actually, easier than it looks at first), if you plan on doing much mod experimenting, it behooves you to look into that MultiSH4 that I linked you to above. All it does is create other Save folders of your own naming, which allows you to keep different game installs separate from each other. Along with it, and another step deeper is Rockin Robbins'
Corruption Management System (SH4CMS). It does its stuff with batch files, which are text-based and easy enough to bend to your will, if so inclined.
One step at a time though. Get yourself some JSGME understanding, get a mod in, and see how you like it. Another important thing to keep in mind is to be sure and install the game in a non-protected folder. When Windows came out with their User Access Control (UAC) back in the days of Vista, they also "protected" more folders from "unauthorized" tampering. Windows does not recognize JSGME as an "authorized" source of alteration. Therefore, when you apply mods to a game installed in a My Programs folder, Windows will put things back the way it knows it should be. I mention this somewhat facetiously, but it does do that. Install SH4 in a folder of your choosing, not the default My Programs.
