Timing Issues

[BigRed76]

First things first here's some basic info on my swap:
'71 C10, 2000 5.3 & 4L60E using factory PCM, factory engine harness modified by me.
PCM setup by Brendan @ LT1swap to run as a standalone PCM.
Only engine upgrades were cold air intake, shorty headers, and dual exhaust with x-pipe.
Also replaced intake gaskets and knock sensors when the motor was out since those are common issues.
Spark plugs and wires are new.
I've had this swap running for a little over 2 months now.

I was previously having an issue with the MAF under reporting, but I moved the MAF farther away from the throttle body and that seems to have cured that problem.

My problem now is I've got what feels and sounds like a misfire...but it only occurs at steady cruising speeds, on decel, and in park It will do it at rpm's above about 1100. I've been watching scan tool data trying to figure this out and I've narrowed it down to my timing. The timing advance is very aggressive, meaning the timing advance goes well into the 40 & 50 degree range, and the misfire will come in when timing hits about 35-37 degrees. And while this is occurring the knock retard is just non existent, so this timing just goes through the roof. At warm idle (600 rpm) the timing sits at about 12-15 degrees. Short term fuel trims are right around 0, and long term fuel trims are right at 4 & 5%.

I haven't really seen much on the net about this type of issue, but from what I have seen stock LS engines don't like more than 30 degrees of timing advance. Are there some other things on the scan tool I need to be looking at or is this a potential tuning issue with the PCM?