Atypical P0304 misfire

Yes, I know misfires on third gen Prius have been covered here many times, but this one is a real head scratcher. I bought this 2010 Prius from a customer because the engine coolant pump failed, overheated the engine and blew the head gasket. A couple months before that it was having a misfire and we did the complete EGR cooler and EGR system cleaning, intake manifold, throttle body, fuel injectors, MAF sensor, new spark plugs, new air filter, PCV valve. It was running great until the water pump failed. I used a combustion leak detector fluid test to diagnose the head gasket which has worked on many other Prius.

I had another 2013 Prius that had a good engine in it was running fine until it had some electrical issue I just didn't have enough time to troubleshoot. All the fuses and everything checked out good but when you would push the power button nothing would happen. Of course I tried a different power button as I have many extra parts around. Tried many things but had to move on to other jobs so I planned on using the engine from that one to fix the 2010.

I did the engine and transaxle swap, I switched over the intake manifold, EGR cooler, all of those parts I had just cleaned out on the 2010 on to the 2013 engine. Also did an oil change, changed the transmission fluid. On its first startup it was running fine so I drove it home that night and on my drive back to the shop the next day I got to check engine light with a code P0304 misfire on cylinder 4. I thought maybe there was something loose maybe a hose had a leak something got damaged during the swap but I was unable to find anything. All the bolts were tight. I had a brand new set of ignition coils so I put those on. It seemed better but after driving it more had the code come back and then it gradually got worse. I used the leak detector fluid and wasn't getting any color change so there were no exhaust gases in the cooling system.

I had another intake manifold and throttle body that I had already cleaned out in the ultrasonic Parts cleaner so I swap those in I also put in a different throttle body. That didn't fix anything so I tried swapping in some different fuel injectors, still got the misfire on cylinder 4. I did a compression test and all four cylinders are looking good between 150 and 180 PSI, all of them identical. I thought maybe something fell inside the engine or something got into there that was blocking the valve or something like that, so I looked inside all of the cylinders with the borescope and there was nothing in there, nothing unusual looking, cylinder four look the same as all the others.

Keep in mind, this engine was running fine in the other car before I had that electrical problem. I inspected the wire harness on the coils, trying to see if one of the pins was backing out or not making a good connection, tried wiggling it while the engine is running but didn't make any difference. Check the fuel pressure, it was good. Of course, if it was something like the fuel pressure it should be affecting all of the cylinders and be giving a random misfire but it's always just cylinder number four. I thought why don't I try the ECM from the 2013 engine, so I swapped that in, no change, if anything it ran worse. I had another ECM from a 2012 I tried that, no change still misfire on cylinder 4. At this point I want to light the car on fire and be done with it LOL but I refuse to give up. I've tried spraying brake clean all around different parts of the intake manifold while looking at engine data from the scan tool, no difference. I replaced the intake manifold gasket, still nothing. I had a customer that needed some new ignition coils on their Prius so I took the new ones off of this 2010 because I figured it doesn't need new ones it doesn't care what it has it's just going to run like crap. I put some coils on it from the junkyard and all the sudden it's running better, not misfiring super bad but when you go and drive it and put the pedal to the floor, at a high load it's still misfiring on cylinder number four.

The only other things I could try at this point is the leak down test but I don't see how it could be a head gasket failure when it has good compression and no exhaust gases in the cooling system. I was wondering if there is something with the variable valve timing or a lifter, maybe something with an exhaust valve. I have another set of fuel injectors that I cleaned out that I know we're working good so I'm going to try changing the fuel injectors one more time. Also worth mentioning I put some good premium gas in with some seafoam fuel cleaner but of course nothing worked.

I've worked on so many of these 3rd gen Prius with misfires and I've always been able to figure it out. Usually it's a ignition coil or EGR system problem. I'm running out of ideas and patience with this one. What else could it be that would only be affecting cylinder 4?

Mahalo for your help!