First install SH3.
Second patch to v1.4b.
Third install JSGME (Run it twice to make the MODS folder and capture a snapshot).
Fourth copy MultiSH3 and SH3Weather into your install directory. Don't run either.
Fifth install SH3 Commander but don't start it.
At this point COPY the entire folder to something else like C:\program files\ubisoft\mysh3 Leaving behind a pristine, mod ready, install of SH3 you can copy again when you want to try a different supermod or have stuffed your mysh3 install so badly you need to start again.
Install any mods you wanted to try out into the mysh3 folder using JSGME.
Run MultiSH3 in your mysh3 folder and give it a unique 3 letter name for Careers for that install only.
Run SH3 for the first time to create your new career folder structure, exit immediately.
Add '
/l:"C:\program files\ubisoft\mysh3"' to the end of your SH3 Commander install shortcut.
Run SH3 using SH3 Commander, your custom mods and custom careers. SH3 Weather will be autodetected and start right before you enter the game.
Enjoy!
What you'll probably do is say "omg, that's too complicated, forget it!" and run GW 1.1a's wonderful install program which works effortlessly. After you've enjoyed GW to the fullest and/or destroyed your install playing around with other joyous mods (not all of which will work with each other), come back here and try it this way.
It's more work, but it's far more expandable.