Still down after 5 months
 

Update
I had a misfire issue that I posted back in August, I beat up the car own my own for a month and half with the help of this forum. After getting completely frustrated I took the 98 boxster to an Indy shop. He has retimed both heads, found a couple of chaffed wires going to the ECU, and the car was up and running strong........with a CEL. He has tried to wipe the ecu clean and reprogram it, no help, he has tried a "new" ECU from a donor car and now the car wont start. And that's where I am today.

My question is this; Does my current problem have anything to do with the theft system not recognize the "new" ECU?

Yes, the "new" ECU is not being recognized by the immobilizer. The ECU, immobilizer, and the key fob must all be replaced/swapped as a matched set (or you need access to a PIWIS to reprogram them to match).

This typically means that you'll also have to swap the key shaft from your existing key fob to the new key fob so the new key fob can mechanically turn the ignition switch.

Your problem is the ecu, must all be new from Porsche and programmed by someone with the software. It can be extremely costly. Been through this myself. There are NO shortcuts!

If you still have the old ECU getting it repaired may be the best solution. I just went through this with a portion of the system also took out the left bank vario-cam actuator. The computer repair was around 1100 itself but far less than a new one.

Sent the ECU, immobilizer, and key off to Specialized ECU repair in Florida, they bench tested the units along with placing them in a known good car. All check out fine. Their suggestion was to check the wiring. Which is what many of you suggested in the beginning of my journey.

Any suggestions on where to start? Or would it be easier to remove the harness to check it?