Quite simply clay, its more than likely a signal issue. So either interference, a dud pick up, or a dud ecu. Id be tryig the easiest cheapest option first, and by-passing the loom in the car, just to rule out interference (it happens more often than most people realise) then sensors/pick ups, looking at the units themselves aswell as mounting points (cracks etc) then look at the ecu.
If you have everything it needs to run, spark, fuel, comp at the right timing and then it doesnt run when its together, youve either missed something stupid, or its a signal issue, it cant be anything else.