make sure those two wires that branch off the main harness next to the ECU are still connected to their clips. I had the same problem after doing the first swap, that one connector with the 4-6 wire connector is what you need to be clipped in.
Turn your key to "on", and see if you have a light on the ECU, and if it will report error codes. If it does, then nevermind my suggestion isn't it. If you don't get a light on the ECU or error codes, check out that wire harness clip.