I would test your throttle position sensor. Since you use lower amounts of throttle most of the time, the electronic guts wear out faster on the low throttle input bands (where you are having a misfire). All they are is a potentiometer that changes resistance of signal voltage to tell the ECU what percent throttle demand there is.
The TPS governs alot of things like timing advance. If you punch the throttle, the timing advances and the injects extra fuel for more power/acceleration. However, the throttle plate also has to be open to let in air to allow that to happen. What I think is happening is your engine is hitting a short-to-100% throttle inside of your TPS so the engine thinks you are punching the gas, richening the mixture, not letting in enough air causing the smoke/misfire.