Occurs mostly at idle but also when trying to hold steady throttle. Exhaust manifold and catalytic are new, new ntk o2 sensor, cleaned and also tried a different map sensor, spark plugs/wires/cap/rotor all new. If I unplug the o2 sensor then it will not missfire and drives fine in open loop. fuel trims are going -10%--20%, which I'm assuming is causing the misfire, right?
Edit: also not sure if it's relevant but I am noticing that my dash lights and dome light have a slight pulse to them, not quite a flicker though, and I do not remember seeing that before.

 

Bump

 

This sounds like it could be an alternator issue, or more specifically, the voltage regulator. You could try logging voltage when this is happening and see what it is doing. A bad voltage regulator in the alternator can cause lights to pulse visibly among other things. It can also potentially throw off the injector pulse width, which could be why you are seeing the wild STFT's. Alternatively, you could have some injectors that need cleaning and are dribbling fuel, which could also cause a negative STFT.