Possible that all 4 of the AFM/DoD cylinder circuit wires and the MAF circuit on the same loom but that is the reason for the poor running. If all 4 of those circuit are left open the engine is likely to default to running on the other 4 cylinders.

I'd be tracing wires and doing some inspecting to see if something chewed through that harness or if it came unplugged or something.