Hmm.. You've shot the 0331 head.. MAYBE somethin to do with the notoriously weak spot between 3 and 4? Idk..

 

Don't make it complicated - it' not rocket science or mystical.

If you use a laptop with a data link and good software where you can see "into" the PCM you'll see "RPM COUNTS"
That's the part where the PCM looks at each cylinder's contribution to the RPM. It compares cylinders when it's running at a constant RPM.
If it's off by much it sets the code. It is not measuring spark, or fuel, it's simply RPM change.
A fuel or spark misfire or a mechanical imbalance, like compression, can set it off.
No other sensors affect it directly.

 

Well everyone I figured out my misfire problem.........I replaced the valve springs and it has been running great ever since, so my guess is that one or both of them where weak and not sealing the valve good and tight.