This tune runs weird. You have the IMRC set to stay open in the tune. The tune is following the mapped points real strange. It's idling in mapped point 14 and uses the lower MP during WOT. This is causing your engine brake torque to be 130 - 160 ft lbs WOT. Is this how you're wanting to run your truck? Your WOT/OP needs to run in 14+ or you can run 14+ all the time, then your shift torque reduction tables will work as they should. Maybe the reason is because SD isn't correct? Something is causing your load and torque to be half of what it should.
You've increased the correct areas like you should, but the calculation is so far off, your increases aren't have any effect at all. I would definitely disable 0-13 and run 14+ if you're going to keep the IMRC's open. The same thing happens in 2>3 shift except your torque is around 160 so torque is reduced to around 80ft lbs by spark reduction during the shift.
atorquereduction.png
Your low load is why spark is sporadic as well. The timing for the load is good, you could have more advance at those loads, but your load should be at least 20% higher. You're at 55% load, 75% load would be running less timing and there would be no KR.