What about the actual spark plugs, did you replace those?

 

Plugs looked good. They are NGK platinum and were replaced about 40k km ago.

I guess I could pull them with coil packs attached and check the spark.

 

I would, hold them with the ground strap of the spark plug 1/4" away from the intake manifold while someone else cranks the engine so you can watch the spark.

Be sure to pull the fuel pump relay first and let the engine start/stall out otherwise it's going to be a mess spitting out gas and running on 5 cylinders.

And wear dry leather gloves, hold the spark plug by the coil pack end or it'll light you up pretty good.

 

Update. I scanned for codes again and sure enough there was a soft code for the Intake Air Temp sensor (P0113).

I checked and made sure the harness to the MAF was good and was getting power. Next I checked the resistance for the IAT. Sure enough, the resistance was way off spec. The FSM states minimum should be around 1.800 and I was only getting around 1.200-1.300.

Went ahead and ordered a new Hitachi MAF. After plugging it in the stumbling has gone down considerable, and at idle there is no more stumbling at all. I can still feel a slight miss at around 1500 - 2000 RPM but it is much less frequent now and not as pronounced as before. The car feels a lot more responsive from 3500 RPM up to redline. I am hoping that after a few drive cycles it will all be good. I plugged my code reader in again and there was no codes, but the monitors have not completed as it is still showing yellow. I hope this is the final chapter of the saga.