Originally Posted by McSteel
There is a way to fix it. When you said "the boot record seems to be on the second IDE drive and not the one with the windows partition on it", did you mean the 100MB recovery partition? If so, that's not really an issue.
Windows places it's bootloader (bootmgr) and it's boot configuration (BCD) as well as the memory testing tool (memtest.exe) and some other tools on the mentioned partition, and marks that partition active. You could freely copy them to the root of your new (cloned) C: drive, make that partition active, and this should work. Couple of things to remember:
You'll need a live OS or another computer to do this. Windows will lock the bootmgr and BCD files for obvious reasons (tempering prevention), so you won't be able to even copy them anywhere from within their owner's OS. If you wanna spare yourself the hassle of moving HDDs between different PCs, or if you don't have a second PC, you could download and burn a Hiren's Boot CD, then boot from it and load Mini XP, then work from there. Be sure to assign a drive letter to the System Reserved partition so that you can copy stuff from it.
The System Reserved partition contains a superhidden "Boot" folder with subfolders and some files, and a superhidden bootmgr file in it's root. Copy both to your cloned C: drive. Use any tool you like to make that partition active. Diskpart, bootice, windows disk management, anything works. Once you set the drive as the primary boot device in BIOS, you should be able to boot your win7.
So it's not just a hidden file I can just copy to the other drive? Drive C: has my OS and is on and IDE cable, drive D: is also on said cable and has to be first in the boot sequence or I get an error. Drive E: Is the clone of C: on sata, and Drive F: is my 1tb main storage drive. I Want to drop C: and D: out of the system, but the cloned drive gives errors, wont repair and wants me to completely reinstall which I don't want to do. So using that Hirens will allow me to copy the files needed and I can then disconnect the other drives and have drive E: boot now as C: without any issues? BTW I'm on windows 8 now if that matters