1996 Chevy Silverado Tranny Rebuilt - Continued issues

Hi, I had my transmission rebuilt by a local shop, the R & R'd all the parts, clutches, switches, wires, ect. as they told me. $1700.00 worth, supposedly with Heavy Duty parts. 1000 miles out of the shop the trans started slipping again while towing a 6x12 enclosed atv trailer. Retruned truck to shop where they say contamination from radiator/ trans cooler leaked and contaminated the fluids. They rebuilt the tranny again and by-passed area of leakage. No visible radiator leak to outside of vehicle. Short time later after repairs made 2nd time, Service Engine light came on - stayed on, returned to facility and found code to be Manifold Pressure Sensor issue. I could not return truck to shop for 3 weeks due to out of town business. Another 700 hundred miles or so later after towing mt trailer with no problems 200 miles. I loaded about 600 pounds in trailer and towed about 3 miles. Engine started running rough, popping, sputtering, check engine light flashing. Could the Manifold Pressure sensor malfunction cause the engine to run rough or is the poor engine proplems causing the tranny issues. Thanks