That is not my experience. Do this experiment: Remove a spark plug wire and run it and see if you get a MIL and code. I will bet that you will always get a code because OBDII is very good at detecting misfires.
It is more likely a fuel delivery problem, especially since you have replaced nearly everything on the ignition side with no effect. If you rev it when it is parked does it still have the stumble or is it only when it is under load?
OBDI or II can code, and usually does. However, when spark is blown out or weak, it usually doesn't code, especially with single coil OBDII. The ignitor sends the signal back to the ECU saying it fired the plug, but ECU can't detect whether or not the spark is proper (complete). Later OBDII coil over plug systems are more sensitive to misfire codes, because dwell is assigned to each coil. But I see bad plug fires without misfire codes regularly on turbocharged COP applications I work on.
Bad ignitors can cause spark leak of a coil fire, and cause the coil to fail. Just BTDT replacing a bad with a known good coil. When the problem didn't go away, I did an actual spark check and the spark at the plug was weak (more fires to ground than to electrode). Spark plugs themselves looked fine (BKR6EIX). New cap and rotor, wires ohmed out fine.
I replaced with new hotter copper plugs (Bosch FR7DC+ to do diagnostics), better, but not solved. Put it on a Sun Diagnostic Scope = weak spark on all 6. Replaced ignitor and coil, problem solved. Both bad factory coils BTW, passed the primary and secondary ohm tests. Just today, I put back the BKR6EIX in fact.
The best test for this is to use an older scope type diagnostic tool. It will show spark energy pulses. I personally think this is a weak spark, likely caused by coil, distributor cap, rotor, wires or plugs. Fuel MIL on OBDII will throw a code (especially with SC) faster and more consistently than ignition problems. Once you are out of Long Term Fuel Trim Value, it doesn't matter what caused it, the CEL is on. Because the danger of melting cats is really high. If fuel caused the running problems described, I'd expect Lean Mixture with Knock sensor codes, or rich mixture out of range + white plugs (lean) or fouled plugs (rich) respectively. The pics of the plugs don't show either.
LTFT = Long Term Fuel Trim (Rear 02 sensors)
STFT = Short Term Fuel Trim (Front 02 Sensors)
With the stock FJ80 Coil at 37kv, I would stick to the factory .8mm (.032) gap. Wider gaps make coils work harder.
Cheers and HTH
Scott J
94 FZJ80 Supercharged