I am in the final stages of a 4.2 Atlas swap into an FJ80 and am having issues with the 4L60 transmission. The engine and trans are from a 2004 TB. The engine starts and runs fine but the trans will not go in gear. The scanner is reporting: trans current gear = 3rd with the key on and 1st with the engine running (no matter what gear I select with the shifter)? I have tested the signals from the transmission selector switch to the ecu and everything is as it should be.

Any ideas?
Thanks
Rory