I'm having problems with windows, it's been bugging me alot, my 700MB drive is the favored dumping grounds for temporary files for any of my programs that use such a feature (even if I tell them to put the temp stuff somewhere else). Tha'ts one reason for switching, anyother is that it's a slow drive. Eitherway, I've used the DOS sys command (sys C:\ D when both drives were in, and I've hard-copied the C: drive onto the D: drive, but when D: becomes master I get a non-bootable disk error.
Recap in english: Small drive contents put into big drive, big-drive has everything it should need to be a boot disk, but still doesn't act like a boot disk.