It sounds like you tried installing mods, and when they didn't work, backed them off? After doing that, did you delete the Save game folder? That is usually "C:\Users \UserName \Documents \SH4 \". The game uses a lot of the information in that folder to run off of. If anything gets trashed in there, then the game will continue to cause you trouble, even after re-installing everything.
Now, a Steam game defaults to installing in the "C:\Program Files (x86) \Steam \SteamApps \common \GameFolder", which is considered by Windows to be a "System" folder. As such, the older games that use JSGME are not "authorized" to alter the files, which if you're trying to activate mods, they are being partially disabled by Windows security. The only way around that is to install the game in a different folder of your making. How you do that depends upon whether you have a 2nd usable hard drive or patition (you don't want to use the computer's Restore partition), or if you have just the one drive most laptops have. See the Steam Knowledgebase article "
Moving a Steam Installation and Games for more information on that, if you're wanting to mod your game.