Actually any of the supermods fix many of the problems that remain. None of the supermods, including Game Fixes Only, fix them all, heck, they haven't all been found yet!
SH4 is a great game because we have several healthy, co-equal competing/cooperating supermods: Trigger Maru Overhauled, Real Fleet Boat, Game Fixes Only, Fall of the Rising Sun, Run Silent Run Deep, Operation Monsun. They are all installable and uninstallable using the Jonesoft Generic Mod Enabler (JSGME), so you can try them all out without big problems and even switch back and forth at will. None of them insist on taking over your game and locking the others out.
I would proceed as follows: first install the game and patch it to 1.4 or 1.5 SH4UBM. Install JSGME into the Wolves of the Pacific directory. Run it once and immediately exit without doing anything. This creates the MODS directory in the correct place for future use. That is where you'll copy mods to later.
Now before you even play the game, copy the entire Wolves of the Pacific directory structure to a new directory. I call mine SH4 Pristeen. When you initially copy it Windows will name it Copy of Wolves... Just rename it when you're done, then write protect the whole shooting match, directories and files. This way you won't accidentally alter them later. This installation is never to be played, and in fact cannot be. It's strictly a toy box to take uncorrupted files from when you find yourself with mod soup (thank you Kapt Lehmann for the best phrase on Subsim
).
In case of mod soup (you'll know when the game CTDs or starts acting squirrelly), you can just uninstall all your mods, delete all the contents of Wolves of the Pacific except for your MODS folder, copy everything from SH4 Pristeen to Wolves of the Pacific, write enable everything there, reinstall all your mods and start playing as if nothing had ever gone wrong.
All your settings and saved games are elsewhere, so they will still be there. Now you will never have to reinstall again!