Win 7 Install Has Made A Mess

I've had to re-install Windows 7. And it naturally did something completely screwy - 1. Disk 0 used to be Disk 1, and vice versa. 2. Rearranged my Disk labels, and drive letters in a nonsensical way, but far worse, it has labeled my Documents drive as "System, Active" (in MiniTools Partition Wizard it is labeled as "Boot" status). And no, I didn't ask Windows 7 Install to do anything to...