The thing with most mods is to just use them properly. The stock game has issues, and some of the mods make the game better at NOT crashing. One problem users have is not being careful of a mod's folder structure. Some of the mods have several mod choices in their "main" folder. Be sure and read the ReadMe file with the mod. It might be that you have to drag a folder out of the main folder. Grab
JSGME v2.60 and read it's instructions, which I think are in a pdf file... ?? and become familiar with its operation. That helps immensely. Also, when you enable a mod, you can NOT use the old "Save" folder, which in stock trim is C:\ My Documents \ SH4. Anything in there will corrupt a newly activated mod and cause several issues, including crashes. Empty the folder, if necessary.
In my opinion, the best course of action is to read-up on
Rocking Robbins' SH4CMS utility and use it. Restoring the game from something "bad" is much much easier with it. As mentioned above, the educated use of JSGME, and last but not least, the educated use of
MultiSH4 v1.5 to create multiple "Save" folders for each separate "install" of SH4 that you have (I have almost one for each mod), of which, RR's CMS really shines in helping you with.