Your SH3 was destroyed?
Did you use Jonesoft generic mod enabler? If you did I can't see how you could have destroyed your SH3 installation as you can undo any changes.
You can get jsgme here if you haven't already done so:
http://216.235.153.31/u-boot/SH3must/
Also... all you patrols and medals etc are stored in your my documents folder, so its strange that you lost them.
Have you used any mods before? Installing mods over the wrong version of the game often results in a crash. You can get the latest patch (1.4b) here:
http://216.235.153.31/u-boot/SH3Patches/
You have a lot of mods to install. Generally it's always best to use jsgme and install the largest mod, working your way down to smaller fixes.
If you want to make things alot easier for yourself, you can download the GreyWolves Supermod, which includes the majority of the kind of mods you want to install and more, all in one package:
http://mpgweb.de/01/
Be warned, it's big!
Any extra mods you still need can go over the top.
Any more troubles just ask...