Never just move a folder of an installed application. Thesedays Vista and Win7 won't let you do such stuff to the Program Files folder without propper administrator authentication, but it just isn't smart. There are usually important registry settings that point to the folder. If you need a clean SH3 game you have to do a complete rinse and reinstall. For prevention of annoyance, instal the game, as wel as SH3 Commander outside of the Program Files folder next time.
If you want to use the Pato 1500 grid mod with JSGME you have to recreate the folder-structure yourself. You could use the 3000m grid mod as an example/guide on what it should look like. The maps.cfg file might be in conflict with other mods you might have (or will have in the future). But JSGME will advice that it get's overwritten when other mods conflict, so you'll notice soon enough.
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