So you sent the ECU to Hondata to get the K-Pro installed?
If the installation was done wrong, the immo would disable the fuel pump, etc. This is why they are having you check the rail, etc. They may have sent you back someone else's ECU, in which case the immo would freak out, and I'm not sure if that's stored in the ECU or not, so I'm not sure if disabling the immo after that would help or not. I don't know much about K-Pro setups, I'm just giving general OBD2b advice.

Also it's a real long shot, and really not very probable, but:
Check all the connections where the ECU harness plugs in to the ECU, I've occasionally seen a pin back out of it's connector shell if the ECU has been unplugged and plugged back in. Like I said, very unlikely but it has happened.