Hello FTE, long time lurker that can usually find the answers I need by searching the forum but this one has me stumped.

I recently had the 4R100 rebuilt in my 2000 F-250. After the rebuild, I noticed the tranny temp runs 40-50 deg higher than before, sometimes reaching 180+ while empty and 200+ while towing only 3k-4klbs with a 6.0 cooler. The truck struggles to tow this light of a load now, it acts like I am towing 10k lbs all the time. I have had the truck checked out just to eliminate a possible engine issue that may have popped up and it came back with a clean bill of health from Don's Performance Diesel in East TN. Buzz test, contribution test, fuel pressure, ICP, etc all looked good but the truck struggles all the time. I do have a tuner on the truck but all checks were done in stock mode then ran in the 100hp setting.
Below are the details:

Fresh Rotella 15-40, fuel filter, air filter
Fuel Pressure: 68 psi idle, 60 psi WOT
In tank screens checked, no issues.
Brakes checked for stuck calipers or binding.

ICP: will hit 2800 and hold steady 2700 ish under hard acceleration, OD with TC locked up, stock mode.

Will maintain 15-16psi boost, stock, 24psi with tuner on.
New CAC boots and clamps.
Up pipes checked, no soot or visible leaks.

What could be going on in the tranny that would put this much load on the engine? Any help or insight would be greatly appreciated.