Hey Kick!! Ok now we can label this problem as SOLVED. Id actually like to change the title officially now because its done. So yes the new ECU was bad with the same damage so we sent it back. I was able to get a hold of another ECU not sure if it came for a sidekick or a tracker but it was a 2dr 4x4 with a 3 speed auto. I have included the picture of the serial number.
Like the other ECU from a tracker, this one didnt throw the P0335 code! Even better it didnt seem to throw any codes at first. Well let me go through the codes and how i fixed them to get this x-90 on the road. Most codes were found while driving with the OBD 2 scanner plugged in.
So the P0335 was gone with the new ECU
The very first code thrown was a P0304 Misfire at cylider 4: cleared that up with new gas as the gas had been sitting for months.
Next code thrown was a P0500 with the speed sensor; cable broke twice (once due to my routing through tight corners) also had a bad speedometer needle and had to order an entire cluster to fix it. The spring that keeps the needle wound and keep proper speed somehow got all tangled and ruined the gears in the speedometer. This was a problem from when we purchased the vehicle but had not been addressed yet. With both replaced it runs without the code and the speedometer works.
P01715: This was the first 3 speed auto code thrown while driving the vehicle around and not worrying about any crank sensor going off. I looked into your wiring schematics on your site and realized the Park/Neutral switch is wired in the same way as the clutch switch so i was able to find a way to add to the harness. P01715 activates pin 22 on connector C2 of the wiring harness so i applied a cranking voltage to that pin and it fixed the trouble code. It only activates while driving above 45 mph but is a pending code until the car stops at a complete stop then its cleared.
P0740 TCC lock up: picked up this code while driving at high speeds and realized that pin 16 on the same connector C2 needed battery voltage and did the same fabrication. The code never showed up again.
Neither one of these wires were included in the wiring harness. I found an old computer power supply and cut one of the wires with metal connector out of the 24 pin connector. The internals are the same as a wiring harness and you can insert the metal connector cut from the 24 pin computer power supply through the back of the ECU harness and make a connection with the pin. Its actually a tight connection and works after the ECM is mounted back in its original place.
The only other code thrown was the P0400 and to clear it up i cleaned the entire EGR piping from the throttle body to the valve itself even to the exhaust. It was pretty caked but did clear the code.
The x-90 has now passed smog due to the fact they dont take the car over 45 to trip the 1715 code (yes still goes off but clears when vehicle comes to a stopped). The car runs great and is now California emissions legal. I welded in a new cat that only cost me 140 on amazon and is california legal. Thanks again for all your help and i hope this information helps you in some way. Enjoy!