Accord idle and tranny issues

I have a 1990 Accord EX, 116,000 mi., with a couple of quirks and thought you guys might help out! First is the classic Accord rough idle that occurs mostly when the engine is "in-between" Hot and Cold, but is also very slight at warm idle, especially with electrical accessories fired up. Just a light bump up of the RPM and it straightens out. The car is recently tuned, has new front torque strut mount and I have "flashed" the ECU and started fresh. Still I have this issue. Any suggestions?? Second, the Auto tranny is developing a "late-shift" in the 2-3 and 3-4 shifts, not particularly rough, and just late enough to be a nusiance. It acts like it is in the Sports mode, but the 1-2 is fine. The fluid was changed recently, but it made no improvent. Any help is greatly appreciated.