TBH, it sounds like at this stage you've dumped a lot of files directly into your game install. And manually edited files. You should uninstall and reinstall the game. Then download JSGME from
here. Unzip the file and put all the JSGME files (MODS folder, jsgme.exe etc.) into your SH3 main folder.
From now on, any mod you want to install goes into your MODS folder, which is located in the SH3 root folder.
Make sure that the folder structure for the mod is correct. Inside the MODS folder, there should be a folder with the name of the mod, and directly inside that folder, you should see a folder called "Data" and maybe some others. Sometimes it's just Data.
For example like this: steam/steamapps/common/silent hunter 3/MODS/name of your mod here/data
Mod authors are usually really good about having the folder structure properly setup so all you need to do is unzip the file and drop the mod into your MODS folder.
If the data folder is not directly inside the mod folder, the files will go to the wrong place when you enable the mod with JSGME.
Once you've put the mod in the MODS folder, run JSGME and the mod should show up in the available mods list. Select it and click on the arrow icon that points to the opposite window. This will enable the mod in the game. What it does is it takes all the files of that mod in the MODS folder and copies them into the game. But the benefit is that you can also disable the mod easily with JSGME, so if something goes wrong, your install won't be ruined. This way you can try mods you're insterested in without permanently altering your game install.
Hope this helps you out.