Ideas? Misfire after head gasket repair

I'm looking for ideas about the possible cause of my cylinder one misfires in my 2012 Prius. This car had a terrible head gasket leak between cylinder one and two. I replace the head gasket and cleaned the EGR cooler and valve. I did not have the head machined but cleaned it up with sandpaper on a thick piece of glass and checked it with a machinists rule and feel a gauges . I used a felpro head gasket . I cleaned the manifold including making sure the EGR passages were clear. I'm still getting cylinder one misfires on cold start up, including if the car sits for 4 or 5 hours. When doing the head gasket I checked the cylinder Heights looking for bent rod and they seemed the same. I have borescoped cylinder one when cold and scoped it with the radiator pressurized. No evidence of leaking. I've done a leak down test on all four cylinders and it's rock solid. I replaced all the plugs when I did the head gasket and have swap them around since with no change. I have swapped the injectors around and put a new Bosch coil on. No improvement. I've sprayed carb cleaner around all the Junctions of the air system looking for a vacuum leak to no avail. Could it be my ecm? I've got no codes except the occasional cylinder one misfire. Otherwise the car runs great and gets 46 miles per gallon. It is the wagon version. Any other ideas? Thanks in advance. Mike

 

Yes, I think you're referring to the EGR ports in the manifold. All cleaned out and could blow air through all of them freely

 

Yeah, that's what I was thinking but why would it be intermittent? It's behaving like a head gasket issue. But I also pressure tested the system to 15 psi and it held it for hours until I went to sleep last night. It went down maybe 1 psi over 2 hours which I put down to the crappy Harbor Freight connector for the reservoir for the test gauge. I did find a marginal connection on the injector for number one and fixed that. But that wasn't intermittent.

 

Yes it had the P0301 before I did the head gasket. Now that code comes and goes as pending and only once or twice has graduated to a current code. So what I think is going on is that it sets a pending code after the misfire in the morning and then I might have five or six stops during the day and it ends up clearing itself. I was thinking about putting a scope on the fuel injection connector and the ignition coil connector and I have a cheap little scope that I bought recently from AliExpress but I've never used it and have no idea how to hook up a scope

 

It's acting so much like the head gasket is still leaking but as far as I can tell it isn't. I even took a piece of paper towel on a piece of wire and stuff down inside the cylinder through the spark plug hole and rotated it all around and then pulled it out checking for any moisture. Oh and I forgot to mention I've done several combustion gas tests on the coolant. All were negative. Before I did the head gasket this car was blowing white steam out the tailpipe

 

Here's another data point I just remembered. I did change the PCV valve when I did the head gasket. The old one was clicking when shook but a little sluggish so I changed it. I noticed the other day when I had the air hose off that the puddle of oil in the throttle body was back. I cleaned it out and then I checked it maybe three or four days later and there was quite a puddle again. So I ordered an oil catch can but haven't installed it yet. Is it likely that it's blowing excessive oil and that is temporarily fouling the plug on cylinder one? I would expect it to affect all the cylinders. I have gotten the occasional misfire on cylinder 2 but very rarely. I have a xtool d8 so I can monitor misfires in real time

 

I checked the head with a Machinists rule. I sanded the head not the head gasket. I thought about running it until it gets worse and possibly a more obvious cause.

 

Thanks for staying with me on this. Regarding cracks I magnafluxed the combustion chamber check for cracks between the valves and around the spark plug. Forgot to mention that. Thanks for staying with me on this