I have recently finished getting my swap going and am haveing a few teething issues as expected. It is a 5.3 ran from an LS1 based PCM with a full manual 4L60 so no trans inputs to the computer.

My issue is a hard yet consistent misfire/cutout when I get to 5,500 rpm in 3rd gear. The car pulls hard all the way to 6,500 rpm in 1st and 2nd every time but will never stay clean in 3rd. On the dyno it pulled hard and was climbing steady before it cut out and lost ignition signal to the dyno. I know I have enough fuel and all mechanical systems are working as they should. My tuner plans to datalog it soon so we cn figure it out but I wanted to see if any of you all had some ideas. It is strange that it only does it in 3rd as there is no communication between trans and pcm other than a speed signal. There is no speed limiter which was my first thought.

Any thoughts on what I may be chasing after?

 

try the crank sensor. Similar thing happened to me only it would happen in all gears but rev fine in nuetral. If the crank sensor is starting to fail this can be a symptom, get an acdelco unit and try it. the crank sensor will cut spark when it fails

 

Just a crazy idea...
I had a similar problem at the track a few times; in my case the engine cut out at 3500 RPM. I deduced it was due to my trans getting hot from hot-lapping, as it ran fine after letting it cool off more. Perhaps the missing trans signal is upsetting the PCM.
What year PCM is it? Does it have the segment for the A4 or the M6?

 

Could the camshaft sensor also be a culprit to cut spark? It is just so weird that it stays clean through 1 & 2.

 

check your fuel pressure with a gauge under load and try to mimick the problem...likely losing fuel pressure

 

There is a trans rpm shift point in the tune. Maybe it is set to low in the tune. I know stock is 5200 rpms on 1999 truck trans.