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Question: Weird Jerkiness after driving 45 min.

I have grandpa's 91 TC with several fairly recent updates, including a new egr valve, egr line, idle sensor, intake manifold gaskets, alternator, wires, plugs, and battery among other things. The tansmission was rebuilt about 8 years ago and runs smooth as can be. After driving the car for a period of about 45 minutes, especially in warmer weather, the car will begin a jerking and hesitate while shifting or when coming to a complete stop. The vehicle acts as though it's going to stall, but never does. Also during this time, the damper door will open and cycle the air through all the openings before returning to the designated selection. This jerky routine will continue for the duration of the drive once it has started and can be temporarily pulled out of it by punching the gas. When the vehicle is parked and idle for several hours, the whole cycle starts over. I have also noticed that a fast acceleration or quick move on the highway will also bring on the issue prematurely. In cooler weather, especially during the winter, the car drives and shifts 100 % normal. The car is not overheating during any of this, and fuel economy averages about 18.5 mpg. I am at a total loss for what is causing this craziness. It has gotten to the point where I no longer feel comfortable even driving the car much over 25 minutes. The car was taken to a shop last year, and the codes were only indicating something with the brakes and the egr. The egr was replaced and the brakes operate normal. Does anyone have a clue how to resolve this rather bizzare quirk and what is causing it ?