I used too have the same problem it could be the wires of the spark plugs or o2 sensors

 

It sounds like your luck is better than mine. My misfire code is in because i have a broke head and several broke inner springs on my dual springs!! Rocker pulled a chunk out the head!!

 

I've seen more then a few nnbs 4.8/5.3s have a poor seal at the valve face and valve seat. What cylinder is missfiring? Isolate the cylinder that's missfiring. Also if it were an ignition problem it should be a constant missfire from idle to wot.

 

well i found out it WAS the 02 sensor .. took it to charlie he hooked it up ... also gave me a little more fine tuning since the stall ...

thanks again charlie .. best tuner ever ...