Since I had heard there were many challenges around re-wiring an original harness for use with a modified PCM, I were prepared with spare PCM’s, Scan Tool and a SCT Flashing tool, prepared with tunes that would remove the PATS system ( the anti theft system that prevents a Motor from starting, if not started with the original PATS key.) I even had a Autotap Commaner that would allow myself to re-program the original PCM. This is the Sniper hardware with PC software from Autotap. I also had a second PCM harness and a second Motor harness, and the donor car’s Wiring manual, so I were well prepared, including the skills from my work for living with Process control computers.
With everything wired, and the battery mounted, and the PCM disconnected, the first test were to pull all fuses, and apply power, by connecting the positive, to look for sparks. It was no spark, so no short. Then with the fuses in one at a time, doing the same, still no sparks when connecting the battery voltage to the main harness.
Now with the key in the IGN position, and touching the battery positive to set the harness alive, there were no wild fire sparks, so time were come to measure that I had supply voltage at the 3 power supply terminals on the PCM connector. Ground connections were already checked.
The time for the big moment were arrived. Plug in the PCM, connect the battery, connect the Scan Tool and turn ignition on. At this stage I wanted to see water and air temp, and throttle position sensors basically working on the PC. This would be the test that the PCM is sort of operational. However, the Scan tool would not connect. What could the problem be ?
The first thing that striked me, was that the PCM do not work. As I had multiple 1997 MarkVIII PCM’s , I disconnected power and replaced the PCM. Still the same.
Now was time to check out the wiring of the DLC connector ( OBDII / diagnostic connector), but it appears to be correct wired according to the 1997 MarkVIII wiring manual.

This is the minimum wiring between the DLC connector and the 1996-7 MarkVIII PCM, including power supply.
Since I also had the SCT XCal-2 device to flash ( re-program ) the PCM, I wanted to try to see if the XCal-2 would connect. The XCal-2 is capable or reading the diagnosic codes, as a scan tool, but the same thing happened here. It would not connect.
What could the problem be ? The 1997 Models introduced the PATS system , could it be such that the PATS also prevented me from connecting to the PCM ? I made some queries about this on an appropriate forum, but several people stated that the Scan Tool and Xcal-2 should connect , even with a stock PCM with no PATS system.
What a heck , could it be, it just should work….. I looked at the wiring manual for DLC and PCM and compared the wiring for 1996 and 1997, and found that a 1996 PCM should “work” in my 1997 harness, even if many sensors would be wrong, as quite a few pins are different between 1996 and 1997. The 1996 PCM have 4 coil outputs, while 1997 has 8 coil outputs, so for sure the 1996 PCM would not be able to run the engine as is, but power , ground and DLC connection matched, so I plugged in a 1996 MarkVIII PCM, and then the Scan Tool connected, and I could see water and Air temp, as well as throttle position on the PC. Actually this was strange as it did not tell me more than that the 1996 PCM “works” in the 1997 Harness , and much of the wiring must be OK.
Is there something that the 1997 PCM is more sensitive to than the 1996 PCM ? Could a bad wiring on some of the in / out puts screw it ?. I would thought no, but if I would put it to the test, it is not so easy as there is no way to disconnect wiring on the PCM one wire by one, in case of a grounding issue as an example. I decided to make me a stand alone system, outside the car, to see if I would have the same problem there as I had in the car. Taking the wiring manual, and a spare PCM harness, it took just an hour or so to wire in a DLC connector, and apply power to the proper wires . The ground wires comes out of the PCM harness and are ready to be grounded. I also connected a few sensors from the motor harness into the PCM harness.
Then applied power , connected the Scan tool, and guess what ?. The 1996 PCM connects and “works” while the 1997 PCM do not connect, just as in the car harness.
Could my 1997 PCM’s all be defect ?..... I bought another Mark VIII PCM on E.bay and got it shortly after. Did not connect. I’m now starting to get frustrated. As stated on the top, I also had a Autotap Commander to play with, but, a lot of strange things happened when I tried to read the PCM, so I thought that it had the same trouble as the Scan Tool and the XCal-2. I contacted Autotap and sniper, and after som E.Mails we discovered that I had a early version of the PC software, and needed an update. I got the update, and attempted to read the 1997 PCM program, so I could attempt to remove the PATS system, and make other adjustments like gear ratio, shift points etc. With the updated software, this tool did actually connect to the 1997 PCM, and were able to read out the program, out of the 1997 PCM. Few minutes later I were done modifying the program, ( simple windows operation, no real programming) , and loaded the program back to the PCM.
I now had the first chance to start the engine, and it started right up, but I do not know if it has any codes , as the Scan tool or XCal-2 will still not connect.
Since the engine runs, and the Commander will connect to the DLC connector, there can hardly be a wiring problem, but could there be a problem with the Scan Tool and the XCal-2 on this particular version of the PCM ?
I tried to contact SCT over their support page, but there have been no reply, but I will make a phone call soon, and ask if they have this experience, and their thought on this.
I also recently found a “paper” on the internet issued by Ford that describes connection issues on 1997 to 2004 PCM’s, where it is suggested to try another Scan tool if it does not connect.
Due to the good support that I got from AutoTap, I have now ordered and received their Scan Tool. This Scan Tool do connect, so I have found that I have codes related to Emmision systems and The AirPump. I have also found that the engine only runs open-loop, and I'm thinking that is related to the AirPump. When the engine starts, it will start the Air flow into the exhaust manifolds, and the PCM , expects to see this on the Oxygen sensors. The bad news is that the AutoTap Commander do not have capablities to turn those systems off , as that is illegal. (!...?)
Since I now have a scan tool that connects, and a Programming tool that connects, it seems that there are a compatability issue with the SCT Xcal-2 and my PCM, not a wiring issue. I have again been in contact with the tuner, and he have agreed to send me an XCal-3 with my files on. When I got that in the mail, I went stright out in the garage, and attemted to connect it. Guess what happened ? It connected without struggele, and few minutes later the engine were running closed-loop, and no significant codes that would turn the check engine light on.
Another good news is that the B&B Electronics that sold me the AutoTap Commander , is taking it back for a full refund, as it did not do what I asked for up front.
The remaining issue is that my Auto enginiuity Scan tool will not connect to the 97 PCM as before ( see above) , but that must also be a compatability issue with that tool, as all other tools that I now have connects. This is no longer major as I have the AutoTap SCan tool to use.