If you're wondering how to make a clean re-install, you may want to review this "Sticky" thread
How to re-instal SH4. It's got some good pointers on doing the job right.
I know you may be tempted to keep your "My Documents/SH4" folder with the saved game points you've made previously, but you shouldn't. Just figure these files are meant to be deleted. You should do so, to keep from messing up the works of the new re-install.
If I were you, I'd make sure the mods you wish to use were freshly downloaded too. This would insure that they are as expected. When you add JSGME to the "Silent Hunter Wolves of the Pacific" main game folder (wherever you decide to put it), open JSGME, this will create the new "MODS" folder in the main game folder. While the app is open, take the "Snapshot" found under the "Tasks" menu heading. This will set you up for checking your main game files in the future.
Expect to have a couple of files always added to the main game files when you run/play the game. One is called "SI.bin" (although I'm not sure, this must keep some of the game settings in it's files). If you remove this file, it reappears after you start the game again. Another will be the images you may take while in-game. Using the "Compare Snapshot" feature, look for files that have been "changed" from the original. These are the files you'll wish to avoid. Make sure no mods are activated when you do the compare.
As I've mentioned, when you use JSGME make sure you follow certain rules to keep JSGME runnung as it should. Never remove a mod out of sequence from the "Mod Activation" side. JSGME tries to keep track of every mod it adds, but it can get mixed up if you pull a mod out of the order it was put in. "Last mod in....first mod out" is how you need to think about the order of mods you remove. Remember that if you add a mod that overwrites a previously added mods files, the last file added is what the game will use. That's OK as long as the mods were made to be compatible with each other. If they wern't, you may lose the intended effect of the first mod......causing problems with CTD's, or unexpected renderings (like the one you see with the OTC radar).
I know there are gamers that like to try every mod out there, having a boat load of them added to the game. I'm of the opinion to keep it simple. If you're not sure what one mod will do to another, expect the worst will happen. It probably will!
