2000 Jeep Cherokee with 156k.
Okay, so I posted a while back about an intermittent flashing check engine light and had misfire codes for cylinders 3 & 4.

At the time I tested the coil pack with a multimeter and got consistent readings across all three pairs. I also took off my fuel rail and switched my fuel injectors around to see if the code would transfer to the new injectors and it was consistent with 3 & 4.

I then did lots of research on my year and found that this year has a tendency to crack the head between 3 & 4. This was over my skill level so I took it and we found that the head gasket was degrading. Since I needed a new gasket I went ahead and had him put on a new head as well since the 0331 head is so prone to cracking - figuring that it would already be off so might as well do it while we had everything taken apart and ready.

I just got it back and I have put less than 50 miles on it and the CEL came flashing on again and came back as multiple cylinder misfires. I'm so lost and confused on what to do. It is running so well and when the light is flashing there are no felt misfires.
I saw that a video where a guy had a similar problem and it was the crankshaft position sensor. Anyone have any advice or similar problems. I am at my wits end.

 

Codes: P303 P304 p300