I already just gave up on this, but I think I figured out the problem previously.
When I cloned it on my desktop the desktop assigns a drive letter to the disk as it is created.
This is recorded in the master boot record, though not as a specific number, but it doesn't match the value associated with the windows installation so it will not boot.
I tried recovery console with the fixmbr and fixboot commands, but in winXP the fixmbr command will not overwrite the previously assigned letter. the fix/mbr command in win 98 will overwrite it, but win98 could not recognize the SATA drive anyway.
After all this I realized I was wasting far more time than just installing windows from a freshly formatted disk. (Installing windows over would still not work b/c the mbr was screwy still somehow).
Anyway those were my adventures, and that also explains why the repair windows option did not work, which was what I originally thought would do the trick. There is a way to set it up in advance, or do it with a bootcd outside of windows that will work, but by the time I figured that out I did not want to spend more time.