what ecu are you using??
the other day my car rb20det with a microtech was running fine, turned it off for fueling started it up and it ran on 4 cylinders. limped home shut it off then started againg and it ran fine...
check your injector loom for rubbed through wires. maybe when you unplug it, it moves the wires then they touch and earth out again??
another thing you can try is swap #1 injector with # 2 injector and see if the problem swaps to #2 cylinder.
you can also do this with coils to find faulty coils.