Mis Fires

I have a 2004 Tacoma with the 2.7l, About 4 years ago when I bought it from a friend I had to replace the head as it had a burnt exhaust valve. It ran great for about 100 miles until I had my tires changed. It developed a misfire that could not figure out, I was still able to drive it but it ran rough and only really seem to like 2000 rpm or higher it smoothed out. Now it blew a head gasket and I bought another remand head. Since it had 287,000 miles and I really love the truck I also did the oil pump, water pump, timing chain and balancer chain with a new balancer pully too. I found out the hard way that Amazon parts are evil, I went through two crank sensors and had to use my old one just to get it to fire up and it still is getting misfires error codes 300,301 and 302. I also went back to my factory injectors after cleaning them and testing them as the amazon one I used were way out of spec (OHMs), My last ditch effort was to pull the complete wire harness out and go though the whole thing and replaced brittle and cracked wires. I also have two ECU's as a local shop told me it was the ECU after having my truck for two months with out correcting the misfire. Has anyone had this issue before, I have swapped coil packs and injectors and the misfires still continue only on 1 and 2, with a OBD computer hooked up with live data the misfires are mainly at idle and clear up around 2000 rpm cylinder 1 has no misfires and cylinder 2 has less.