I swapped motors out of mine and my buddies eclipse. When his car arrive it has a rough idle, I think nothing of it and let it cool off. I go to pull it onto the concret pad and it's idling really rough, spitting and sputtering and shuts off halfway up the ramp. Push it up and pull the motor out. I pull the motor out of his car and my car, clean the combustion chambers out of his head and put his motor in my car; cranks up and idles fine. (Weird I thought, ran fine no CEL's without me even changing spark plugs, I pull my car out and his back up) Install my motor in his car and the car will not start. The car isn't getting spark, sounded like the fuel pump wasn't priming in the beginning either. On my motor there is a new crank position sensor, that has less than 2k miles on it (I wired it into his harness and his old connector into mine) check wiring a couple of times to make sure that everything is correct and it is. Keep in mind both motors ran before the swap, his was rough but mine was perfect. So I check again, no spark. Checked the ASD/fuel pump relay, they are good. Change the cam position sensor back to his and still nothing. Change coil packs also, nothing. His ecu harness appears to have been cut at the very top and the top three pins are not connecting, but before I go and find a new harness (from a dodge avenger, with a 420a, this will work fine right? The harness is the same size and appears to have the same ecu) I am quintuple checking to see if you guys can come up with anything. Any help at all would be greatly appreciated.

Is it possible that a little bit of water inside the VSS would make it to where the car will not start?