WELCOME ABOARD!
It's only complicated because it's new to you. Once you understand it it's a breeze. I know, because I used to refuse to use it for the exact same reasons.
1. Is your version of SH3 1.4 patched? to find out, start the game, and at the bottom right corner of the loading screen it should say v1.4. If not, you'll need to download that patch.
2. Did you play the game at all before trying to install GWX? GWX must be installed over a fresh 1.4 install of the game itself, or else it will have problems.
3. With JSGME you need to install one mod and try it out. You don't have to do that every time, but some mods overwrite the files created by other mods, so if you installed something after New Interiors or Open Hatch the newer mod may have shut off the open hatch functions.
4. You say you created a MODS folder within the SH3 folder. Did you install a copy of JSGME inside the game folder as well? If you did it should have created its own mods folder, and if not then the game doesn't know the activated mods are even there.
I could be wrong, but it sounds to me like you tried to do too much all at the same time. One thing at a time, please, and we will be glad to help you each step of the way.