A couple months ago while driving 30 miles to work my wife had a flashing check engine light that came and went. On the way back home the light came on permanently along with the VSA light and and exclamation mark. The car started running poorly for her (after driving 60 miles or so). Once she made it home I threw it on the code reader and was getting P0300, P0301, P0303. I did a compression test, no compression in cylinder 1. I pulled the head off and found a burnt piston in cylinder one and a fair bit of damage to the cylinder wall. I managed to track down a JDM engine (approx. 40000 miles on it) and installed it. I had to use the exhaust manifold, Vtec solenoid, intake manifold, crank shaft position sensor, ac condenser, alternator, power steering pump and EGR off of the original engine. The fuel rail, injectors, brand new spark plugs and coils are all new off the JDM engine. The install went great and the new engine sounds and runs great at low speed and idle. However, the same problem seems to be happening, misfire at highway speed under load around 3500-4000 rpm. The only codes I am getting are P0300, P0303, P0304 ( sometimes only P0303 ). Different cylinders then the original time but I am assuming from the same cause. I have checked fuel pressure it seems normal. Cleaned the MAF and MAP sensors, cleaned the PCV and the EGR. Disconnected the catalytic converter and ran it, same miss fire at highway speed under load. I have checked the fuel trim and it seems normal. I am running out of ideas! Any suggestions would be appropriated, thanks in advance. I havent checked the valve clearances yet but I just think it is just so unlikely that both engines had bad valve clearances. It is on my list to check though.  Basically the car feels underpowered when trying to accelerate up a hill at highway speed and then throws the misfire codes.