Does your scanner allow for real-time misfire counter? Might want to see what's happening. Could be the plug/coil or even compression. You might want to check compression ...esp on the #3 or #4 cylinders (esp #3) to see where things stand. And throw an oil pressure gauge on the engine.
What happens on these engines, is the oil pressure goes low, oil doesn't squirt under the pistons like it should. Cylinder temp goes up, and exh valve gets burnt. Center cylinder often. Not saying that's your issue, hopefully not. But it happens. Mine has all that. Lower compression on #3. Oil pressure is a hearty 11 psi at lowest idle (24 going down the road). My engine's misfire counts go up. If they go up past a certain threshold ...I forget what that is right now, it'll light off the C-E light. But it doesn't put it into limp mode. Mine's usually slightly under the threshold. Probably been like that for who knows how many years??! 5-6? Again, probably something else...but worth check them out if need be.
The solution when ya have that condition is to pull engine, install new bearings and oil pump kit. Replace the affected valve/s. If it weren't for the few weaknesses these engines could go forever.