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?