Unusual immobilizer problem

Hi I need help with this. I break these for a living so have some working knowledge. I have a WJ 4.0 petrol/lpg 2001 (car A)faulty, was running perfect then immobilizer light would not go out, engine turns but no start.I have a donor car was running fine but seized engine (car B)so transfer ecu,key and transponder from A to B, key recognized immobilizer light goes out. Also transfer good ecu,key and transponder to car A, key not recognized. Have transferred the following good components from B to A, alarm module, fuse board and body control, alarm sensor, dash clocks no difference. Earths checked under centre console, near fuse board under hood and from battery and ok. It seems to me that the problem is between the transponder and the ecu but im at my wits end how to progress now, can anyone help. The only other oddity was the dash was acting up a bit prior to this but a self test proves the clocks are ok. Any ideas, thanks shay