2006 Honda civic hybrid ECU problems.

[AnoxieGTO]

Ok I have a 2006 Honda Civic Hybrid i have rebuilt it was hit in the front, and the block ended up busted so I got a parts car that was rolled the engine and Tranny came from a 2007. The ecu was busted so I got another one. When we got the car ready we turned it over and it shut off as expected because of anti-theft. Took the car to Honda to have the computer reprogrammed to accept the security stuff. Next day Honda calls they can't communicate with the computer. So they do some stuff (he said he disconnected modules) call back still nothing. Then he thinks the computer is bad. So I get another one...nothing. Then He wants to try a 2007 Computer...nothing. I have swapped the engine wire harness from 2006 to 2007 harness nothing. I went and got the car because they weren't helping much other than process of elimination fixing which I can do or have done for way less than 85.00 a hour. I have purchased the main wiring harness that runs around the engine bay into the car and plugs into the computer. I am about to try changing those.
The engine was running before we took it out of the donor car. I heard it myself. When I hook up my obd2 code reader I get U0100 4 times. If I try to clear them they just stay on there. I know that code is Lost communication to ECU. I'm thinking there must be a cut wire or something on this main harness but before I go through all the trouble of changing it I want to make sure this is the next logical step.
Also should I use the 2007 Ecu and engine harness or the 2006 ecu and engine harness?
Thanks for any help on this I am about fed up with this car been working on it 6 months.