OK, so my primary Hard Drive seems to be dying with a controller failure of some kind, as per my unhappy event log running up to a crash a few minutes ago. Additionally, the BIOS failed to detect the 1st HDD when I reset the computer (I had to completely cycle the power for it to reawaken).
To be fair, these crashes have been happening regularly for maybe two weeks now (and it seems to only be when playing games, for some reason) and the first instance of these errors is apparently two months ago (!). I've spent the last two weeks elimnating every other possible source of the problem (drivers have been rolled back / updated, SMART is fine, chkdisk fine, surface scans on the disk are fine, can't find any malware).
So, what I'd like to do is move my C: to my second hard drive and just boot from there, without removing any data on the second drive. So, I'm going to remove a 50GB partition on the 2nd drive that I no longer use and shrink another, leaving 100GB free at the end of the drive for C: to be copied in to (while it's much bigger at the moment, it is mostly free space and will fit in 100GB).
Roughly as per this diagram (so I don't have to spell out my entire drive config):

Getting the partitions adjusted and the data copied is, frankly, the easy part.
What I want to know is, exactly how would I get then Windows to boot from the copied data?
Ideally, without having to open up my case (it's a real pig to get it out of the desk, etc), I'll just be disabling the first drive in the BIOS and pointing it at the second.
Update
Disk 1 in the image above is, thanks to me paying around several months ago if I recall, a windows Dynamic disk so copying partitions has proved more taxing than expected. The plan (already half way done) is to shrink the C drive, then copy D to the end of that drive before rebuilding disk 1 as a Basic disc and copying both partitions back.