2002 Jeep Cherokee cylinder misfires

I have a 2002 Jeep Grand Cherokee 6 cylinder inline 4.0 litre. Engine light was on. Checked it and it said cylinder 1 and 3 misfire. Checked the spark plugs, injector wires, coil rail. Did a compression test, everything checked out except cylinder 4 stopped at 135 and then by turning the engine over a few more times it jumped up to 160 (where all the other cylinders were at)
Checked into cylinder 4, lookes like it had been honed out at one time.
Plugged into the scan tool again and cylinder four misfire code came up, changed the injector on cylinder four.
Still was running rough, scanned it again and now it is coming up as Cylinder 4 and 6.
Its all over the place. Changed the plugs thining maybe the we put the original plugs from cylinder 1 and 3 into cylinder 4 and 6 and maybe the porcelin was cracked causing a spark in the wrong location on the plug. No still running rough.
Engine light hasnt come back on yet but im sure it will once I drive it. What more can I do?
Could it be electrical and if so than what?