This is what I did. I added a Download links to my favorite center.
I burnt all reliable mods onto a dvd, original zipped and my Mod folder. This way if something happens all you need to do is copy paste your dvd mod folder to your SH3 JSGME Mod folder in SH3 folder. Also you have a backup should your computer bugger up or SH3 stop working.
I would use a rewritable DVD so you can update it.
Check for update time to time. Thats all folks.