Could it have to do with a load (In drive) and being at such a low RPM when stopped at a red light. Gonna get the coil paks checked. I'm a preventative maintenance freak, so any suggestions are welcomed especially at this high mileage.
A well-sorted automatic should be able to idle effortlessly down to 500 rpm. I'm not sure I understand the issue you are describing, but it seems like the car idles smoothly in Park or Neutral, but "stumbles" when you shift into Drive. The OBD-I idle control system on the 1994 NSX works through the EACV, which is a solenoid-activated air bypass valve that opens based on input from the ECU and its related systems. When you shift into Drive, you connect the engine to the torque converter, which introduces a load on the engine. To maintain a stable idle, the transmission computer should send a signal to the ECU via the shift position switch sensor, and the ECU should then command the EACV to open more to compensate for the load. The first thing you should do is test the shift position sensor signal to make sure the ECU is getting the right information. The procedure is on pages 11-76 to 77 of the service manual.
If you have a good shift position signal, the next step is to test the EACV. The procedure for that is on page 11-70 of the service manual. Assuming it checks out ok, I recommend removing the EACV from the intake manifold and thoroughly cleaning it. I always replace the filter screen and o-ring and clean out the valve body with throttle body cleaner (make sure to tilt the valve so that the cleaner drains AWAY from the internal coil).
If these steps don't fix the issue, I would make sure your idle is set correctly and your idle screw and passage are perfectly clean. After removing the throttle body, remove the idle set screw, counting the number of turns.
Thoroughly clean out the idle air passage with carb cleaner and a non-marring bristle brush. I replace the idle air screw with a new one from Honda, since it is cheap (like 12 bucks), it is pre-coated with the factory red sealant and comes with a new O-ring. The part number is 16016-PM6-005. Install the screw the same number of turns as the old one and then go through the idle set process, which is on page 11-84 of the service manual. Do not rely on the tach in the gauge cluster- you should use a tachometer connected directly to the pickup in the engine bay. Per Honda's spec, the automatics should idle at 600 rpm (+ or - 50 rpm) in no-load condition, which means that the car should be in Park and none of the following items should be operating: headlights, blower fan, rear defogger, radiator fan and A/C compressor. I just shut off the climate control for the test and make sure I measure rpm when the rad fans aren't running, since the car will be warmed up. Once you get a good, solid idle, seal the idle screw in place with some clear silicone.
Hope this helps.