Hi i have changed the engine & box on my lse gone [ down to a 3.9 ]
i was careful not to remove to much wiring ect just changed the hardware !.
now the immoberliser will not let me turn the motor over on the key .
have done the test in the book of words but have not got a flashing led
remote fobs work ok . done the built in test procedure still no reaction
kind of out of my depth now .
any suggestions !!

where abouts are you, does help as some of us maybe near to come and help

Hi i am betwixt hereford and abergavenny . on a hill in the rain

Hi did you ever get it sorted, if not I had a similar issue
If you changed to a manual box like I did you could be having an issue with the jeep thinking that its not in Neutral/Park as if the auto box was still connected.
Under the bonnet and beside the ABS servo there is a connector that is for the gearbox wiring, if you earth the black/yellow stripe wire to the N battery terminal it might help. This tells the ECU that (the now gone auto box) is in neutral and the engine should fire up. This had my head wrecked for ages.
If this helps great it was the solution to my problem. Click on the link below I uploaded the page from the electrical troubleshooting guide that helped me
https://docs.google.com/open?id=0B2div2XAqqt6VjFudElMWVVHcHM