I am posting this hear because there appears to be so much expertise around PCM’s and alterations that someone may be able to point me in the correct direction. I have a 2001 with a PCM which contains a flashed chip (stock motor). It has been acting erratic so I decided to put a stock PCM back into it. I have put two new PCM’s into it with the same result – They both trigger the Immobilizer light the moment the key is turned and will crank but not start (disables the ground circuit for the F/P relay, the coil circuit and a few others). My research indicates this early light means a key/ immobilizer mismatch as the CPM will not register the Key. BUT with both CPM’s I swapped out the complete CPM, Immobilizer, Keys, and Starter Switch with Halo. When I try them on another vehicle they fire up perfectly (one was from a 2001 and the other a 2003).

This points to a problem with the Harness. I have the 2001 shop manual and the Miata immobilizer training manual and have run all the tests on the circuits they indicate with nothing out of spec AND when I put the Flashed PCM and related parts back the car fires right up?!.
Incredibly perplexing. There has to be another circuit unrelated to the immobilizer which is messing up the new CPM's but I can’t imagine which. I have checked the ground circuits and they are okay. Does anyone have any idea what additional circuits related to the CPM that may be the culprit here?

 

It appears my post has failed to generate much interest but I do have an update. A bit of dumb luck - I was rummaging through my heap of spare parts and I came across a complete intact engine harness for a 2001 I had forgotten about!! I think it covers most sensors with the exception of the FTP and I have a manual transmission. This harness does of course tie into the side harness' but that tie-in does not compromise the connections between the majority of sensors which are direct to PCM with in the harness. This still leaves some question around the Immobilizer of course but if needs be I can run a direct line from the immobilizer to the PCM! With some luck I may narrow the culprits today or maybe even resolve the problem.

 

If you have swapped the complete set (PCM, immobilizer module, keys, locks) each time and they dont start (whereas they were starting the previous time with the "chipped" PCM), then the sets swapped do not have matching PCMs/modules/keys.