I'm a little stumped on where to go next with this misfire I'm chasing. It comes and goes. First time I pulled the code, it was a random misfire on cylinders 3, 5, and 6. Second time, just 6. Third time 3, 5, and 6 again. Some days it runs perfectly and does not misfire, others it comes and goes constantly.

MAF is clean
Spark plugs look great
Swapping coil packs doesn't change the cylinders that misfire
Swapping wires doesn't do anything
Cylinder 6 got a new injector last year
Fuel filter was replaced last year as well

Also the truck sat for about a month before this all started. Put a can of sea foam in the gas and fresh gas seemed to help a bit but it's still missing.

Any ideas on where to go next?

We chased intermittent misfires for a while.

We replaced plugs and wires and that helped but did not completely eliminate it.

We finally noticed some carbon tracking on one of the plugs and replaced the plug boots attached to the coil packs. We did not replace those when we did the plugs and wires the first time.

Thats what worked for us.

Excellent troubleshooting, sir. A simple ground issue that the novice would never think of. It pays to be observant...