Hi,
It's not a good idea to try to run a old saved game after a installing the game. They just don't play well together. You should delete the folders that have stuff from an old install. And when you install JSGME, before adding any mods, take a snapshot of the game located under 'Tasks' of JSGME. Also I recommend that when you download a mod(s), save it somewhere in documents under in a folder. Copy the mod to the mod folder that JSGME made in the SH4 folder.When or if you have to install the game again, these mods in in the documents folder are not corrupt. Hope this helps! Also someone wiser and better qualified that me will be along to help! Good Luck!