Going to leave this here for future reference, This is exactly what my AW4 swap is doing.
This was copied from Stu's offroad.
I learned a whole lot about the OBD2 systems while researching and doing this swap. I was fortunate to own an OBD2 scanner. This really helped me work through some issues.
I had been fighting an OBD2 code I kept getting from the tranny. (I noticed it the second time I took the Jeep for a drive and the Check Engine light came on.) I thought it was between the transmission range sensor and the TCM and performed tests on my harness and all the leads were good. I then tried another TCM and I got the same code. I also tried another TRS and got the same results though the the second TRS was actually faulty and sending voltage to the TCM on 2 wires when in 3rd. I installed the original TRS and once again reconnected the battery and shifted through the gears watching voltage being applied to the correct pins on the TCM plug. I did every test imaginable and everything tested out good. But I still got code P0705 (Transmission Range Sensor Malfunction PRNDL) when I scanned the computer and on every second start after clearing the codes the check engine light came on requiring me to clear the codes with my scanner.
Here's what I think is happening. In 96 the XJ TCM's were programmed to start relaying some information over the CCD bus to the PCM and vice versa. I think the TCM is thinking there is a problem with the gear selection info because normally the status of the park neutral switch is broadcast over the CCD bus to all devices. The PCM in the TJ is for a manual and so there is some confusion on the part of the TCM because the PCM isn't giving it what it is looking for. The CCD bus + and - circuits are for communication between all of the OBD2 devices in the vehicle including PCM, TCM, airbag module, and sentry immobilizer key. All of these devices have a SCI transmit wire going to the Data Link connector though the PCM also has a SCI receive wire. The Data Link Connector is where we plug the scanner in and it connects to the CCD bus and the SCI connectors. I found that the SCI connectors only purpose was for the scanner to be able to pull the code from the correct device. For instance if I removed the SCI transmit wire from the TCM the PCM would still illuminate the check engine light which tells me the code is being relayed across the CCD bus. But if you then try to scan for the error code you get nothing. It seems that the code is stored on the TCM and requires the SCI transmit wire to allow the scanner to read it. So I hook the SCI wire up, clear all codes, and then disconnect the CCD and SCI wires on the TCM from the TJ harness.
Here's what happens...it runs perfect!! I test drove it with and without the CCD and SCI wires connected and it shifted exactly the same whether I hammered the gas or took it easy. It braked exactly the same and idled the same. The best part was that I no longer get any error codes when I scan the PCM. The PCM is happy thinking it still has a manual tranny behind it. It gets RPM info from the tach, and output speed info from the speedometer and its happy like before the swap. Now the TCM I think is getting everything it needs too. The tranny has its own input and output speed sensors. So the TCM knows the engine RPM, and of course the output RPM's. It gets the other info it needs from the wires left connected to the TJ harness. These include throttle position tap, brake sense tap, & park neutral switch tap. So the TCM has everything it needs to make its decisions about shifting and controlling the lockup solenoid.
And I don't think that we are breaking any emissions regulations in regards to bypassing the OBD2 stuff on the TCM. Our TJ's never had any OBD2 controls on the tranny prior to the swap so technically I don't believe we are required to integrate the OBD2 TCM into the data link connector.
Now if for some reason the tranny is misbehaving and you want to pull other codes from the TCM all you have to do is hook up the CCD + and - as well as the SCI transmit wire. Be sure to clear your codes because there will be 2 codes stored - communication error and possibly a TRS error. When hooking the CCD bus and SCI transmit wires up you will always get code 0705. Ignore that code. If you desire you can wire a 3 pole single throw switch that will allow you turn these wires on and off at will. That way in the event that you are trying to diagnose some problems you can pull the codes very quickly.