99 problems and a Ford ain't one.

Ok...so you’ve eliminated the fuel pressure issue.

It certainly is missing on more than one cylinder. Usually if you stick a valve it gets bent, especially the exhaust valves. Doesn’t always happen, but it usually does unless you have a mile of P/V clearance.

While you have the heads at the shop (or maybe before you pull the heads) I’d take the oil filter off and it it open and look at the guts of the filter to see if there is any junk in there, and if there is how much and what it is.

Just off the top of my head...if the engine has metal from the first cam floating around in there, that junk will end up in the lifters and it will affect lifter function. Although, even with my ear buds in I couldn’t hear if the lifters were clattering while it was missing. That is due to 35ish rock concerts over my lifetime and literally standing on the starting line for thousands of unmuffled passes. So it could be making noise and I can’t hear it.
Bent valves would be my guess or at least bad seats. Definitely valvetrain related. Oil has already been changed twice since cam swap. The old filters are long gone now. Oil is staying clear and clean. Would sticking/bent valves cause the motor to slow crank or drag? I ask this because there are moments when it would crank normally and then catch and drag real slow and then crank fast again. These pro comp heads have been nothing but trouble. Two of the original springs broke right away. So I switched to some Comp Cams high pressure springs. Either way, heads are going to a machine shop reputable for building race engines.