well not having those plugs connected to the wires isnt going to cause any major problems to the engine...just means ur 1 and 3 cylinder isnt going to fire. i would say u have something else wrong thats causing it not to start. that backfiring was the result of 1 and 3 not being plugged in and runnig on two cylinders. the fact that u had the ecu out and unplugged though could be part of your troubles