I have been experiencing this same issue where my Jeep YJ with Automatic transmission would have a rough idle when driving for a period of time especially in outside temps exceeding 100degrees. Ive noticed this once i put my Jeep in park it would idle smoothly and once i put in drive it would bog down and up and down again like it was about to die. My fix was adding an Aftermarket Transmission cooler to my Jeep. Weird as it seems I had my mechanic check everything from the Cap, Rotor, plugs, vacuum, IAC, computer.....I mean everything until I added the transmission cooler and WALLA.......No more bogging down. My temps do not exceed 200Degrees on my radiator. Jeep runs smoothly at stop signs/lights. So i would recommend adding a transmission cooler if you havent done so. Just my $.02 (Cents) worth.
\m/ Ernest \m/