The PCM cant tell if an individual cylinder is lean. true enough, but it does get the CID ( cylinder identification signal ) passed on to it from both the SPOUT and the cranks shaft position sensor. It converts it through the PCM to base timing and RMP information then redistributes that signal to the ICM which controls the coil packs. So, if the PCM, crank shaft position sensor, or the SPOUT connector were damaged via either straight up bad parts, or frayed or burnt wiring it could theoretically cause a consistent miss fire on the same cylinder repeatedly via fubar PIP and or CID.
Barring an intake leak on the number 3 runner, a burnt exhaust valve, worn cam lobe, or leaking gasket I think I would lean towards the PCM, the CPS, or the SPOUT.
That's my 2 cents any ways.