Crank relearn has been doneMaybe the installers left some things unplugged or damaged wiring from working on your car? Just a thought. I'd start there and make sure everything looks right.
I have heard of sometimes needing a crank relearn after replacing a clutch. Doesn't seem to be every time. Even after I tuned my car I had to do a crank relearn, but remember only one code that came up.