2006 Suzuki Reno Cylinder 1 and 4 misfire

I recently just had to replace the engine in my 2006 reno at 65000 miles, upon having a used engine with 68000 on it, the check engine light has not turned off. I got the codes ran and it says cylinders 1 and 4 are misfire. Had the ignition coil replaced did nothing, removed the valve cover found out the shop put it champion spark plugs so I replaced them with the right ones (ngk) Nothing. The check engine light stays on all the time but everytime the car exceeds 60mph the light starts to flash. I turn the car off and restart it, and it stops, tested it again, drove its for 30 mins at 55 mph no flashing, but as soon as I gassed it over 60mph in about a minute it started flashing again, any ideas, the engine has only been in for less than a month, sounds great but gas mileage is extremely below normal and car seems to struggle with power. Really could use some help.