I just got this 2013 Prius, it was a fleet vehicle and has 390k on the body and an unknown mileage on this engine because it was replaced. Just my luck after a few days I noticed some vibrations around part throttle cruising so I checked techstream and I was getting a cyl 1 misfire. Now I know this usually means a blown head gasket but I tried spark plugs first then I tried cleaning the EGR all within a week but it made no difference. I decided I would have to replace the head gasket so I bought a fel pro kit and got to work. The install went smooth, I triple checked timing before putting the front cover on. I get everything back to together and go to start it and oh my god the horrible rattling like its wanting to shake itself apart. At first it wasn't bad and it actually smoothed out for a few seconds here and there within the first minute then it just began running absolutely terrible. Far far worse than before. I pulled up TS and I was getting a heavy miss on cyl 3. It looked like it was not firing at all. I shut the car off and checked the plugs, plug 3 was wet. I tried swapping plugs, no change. I tried swapping coils, no change. I re verified timing then called it a night. Today I started with a compression check, got them all to 150 psi after about 15 seconds of cranking. Did a leak down, all checked out but cyl 1 had the largest loss of about 5% where the others were below that. I stuck a straw down the spark plug hole and carefully marked where each piston was at their highest. They were all the same. I took apart the intake and flushed out the EGR passage ways because I had not done that when I cleaned the EGR. There was a lot of shit in there. I removed the valve cover and checked that all the valvetrain looked normal. I then bought new spark plugs and tried those. Nothing I did made a difference and its cylinder 3 that basically is not combusting. I have unplugged connector on that coil and the car runs the same so I know it's not combusting at all. I tested spark and thats good. I have not pulled the fuel injectors and test them but I have swapped them. I don't want to just throw parts at it, I've tried testing everything I can think of. The last thing I did was spray some started fluid into the intake to see if I could get it to run smoothly which would tell me if there was a fuel issue. I could not, get it to tun smooth but I did notice theres an exhaust leak or at least it sounds like it by the headers. I had a really difficult time getting one of the middle header studs in, I think I only got it about 75% in then since it was getting very hard to turn and I did not want to snap it and I figured it was far enough in and the bolt would still be able to drive down far enough to clamp the header to the head. I'll look at that again tomorrow maybe thread chase it. I just can't understand how this happened. It ran totally fine before and every test checks out fine. No I did not resurface the head, yes i cleaned all the parts very well. If there were warpage you'd see it on the leak down and possible compression test. What should I check next before throwing the whole engine away.