What I would do would be to try installing MCE on a blanked hard drive,
with the Vista drive disconnected, to see if installation went the same way.
If it did, I'd probably give up on MCE. If it didn't, I'd be able to plug the
Vista drive back in and enable dual boot between the two drives.
There are people more determined than I am who wouldn't give up on
MCE if it did that again presented with an empty hard drive, but would
figure out where to get the drivers that would keep it from doing that.