Roughness after WOT pulls

I have been tuning on my Willys project off and on since June. I have ran the logs through the spread sheet to get the VE tables close. I have an emulator which makes tuning changes a snap. I can run a datalog and run the BLM data through the spreadsheet and then reset the PCM. Drive around normally and everything feels great. Make a couple of WOT pulls to around 5K and then while cruising at 35 to 40 MPH there is almost a vibration in the engine. It happens from about 1300 -1600 RPM. I can take battery cable off to reset the PCM and it will go away until it I make some spirited pulls. I changed the integrator delays to be 1/4 of the original settings and that helped a lot but there is still a slight "roughness" at 1300 - 1700 RPM. There is also a slight roughness at around 2300-2400 that completely goes away at 2500 RPM. Has anyone ever ran into this before? It just seems odd. I'm attaching my bin, XDF, ADX and log if anyone has time to review. I am open to any suggestions. There are some knock counts in this log and I need to pull some timing in a few areas. It was 90 today and I have some knock due to the extra temps. The engine is a TBI headed 350 running $0D and a 16197427.

Thanks in advance to anyone taking time to review the data.
Brian