The wiring harness had multiple serious breaks which shorted the previous ecu. So I replaced the majority of the harness including the fuse panel, but I did not replace the segment that connects the the ecu after finding no visible damage. I should note that the harness came out of a 97. I tried a 97 ecu and I get signal from the computer and it runs on two cylinders. Which makes sense seeing as the coil pack pin out is different on the 99 compared to the 97. But I am still lost as to why the 99 ecu works but only for a couple of seconds before cutting out?