Problems booting after switching contents of some HDD's in Clonezilla

Ok, so I have a 500gb HDD in my old pc (windows xp professional x86), and a 160gb HDD in my current pc running windows 7 ultimate x64. I decided to switch the contents of my hard drives using clonezilla. The 500gb HDD has 2 partitions, one being 375 and the other being 125. I successfully made back ups of my 160 gb to the 2nd partition of the 500gb which is 175 gb big (the backup file is about 90gb) and made a back up of the 375gb partion (back up is about 100gb) to another spare HDD I had lying around. So heres the strange part.

I successfully restored my 160gb on the 500gb's first partition, and it worked swell. I then put the 500gb first partition (About 100gb big) on the 160gb HDD. That didn't workout too well. It really messed up the drive, and became raw and all that other wonderful stuff. it wasn't showing up in the windows 7 Install disk or clonezilla, but it still showed in my bios. I could see it when I went to the load drivers option in the windows 7 repair disc part, and when I clicked on it, it said I needed to format it but it couldn't. I eventually did the "/clean all" and that restored the drive to the normal state.

Back to the new 500gb HDD with the installed 160gb back up. It didn't boot up. I tried fixing the boot sector but it didn't help. I restored it with clonezilla, but I get the same blinking underscore. I tried the bootrec and all the mbr commands and stuff like that and they all said it worked, but I get the same underscore. I know the problem isn't faulty backups, as for when I load the drivers just to check what partitions which, I can see all my files and stuff neatly unpacked. Im just focused on getting my main machine to work. Any suggestions? Im sorry that this is such a long post and is probably hard to understand, but help would be greatly appreciated.