2003 LM4 dropping to 0? of timing when put into gear.

[acidcrashdburnd]

1998 Jeep Grand Cherokee with LM4/60e drive by cable Sloppy Stage Two Cam, NO NSS and stand alone harness.

This is a random occurrence that can remain an issue for 20-40 minutes then it returns to normal.

When I put the Jeep in park or neutral it idles great and most of the time when I put it in gear it also idles great. Since I have built this and even before I had it tuned it would randomly run poorly stopped and in gear. When I finally scanned it I noticed that it was dropping to 0? of timing and ran like a tractor. I have a relay that I use that triggers the brake pedal signal and once that was unplugged it ran fine in gear or out of gear, weird, then last night with the relay still unplugged it started to run like a tractor again. The scanner PRNDL status states D4 when its in drive and will change when you cycle the shifter to lower gears. I have the PRNDL setting set to NONE in HPT. I have a scan of the issue but I currently don't have access to the tune file. Not sure where to go from here, even my tuner has no idea whats going on.
drive-timing.hpl