Mine was acting very similar to what you are describing and kept throwing a P0301 cylinder 1 misfire. Tried checking tons of things to track it down (swapped plugs, leak down test, swap injectors, etc) with no luck as it was fine most of the time. The ignition coil rail finally failed completely one day leaving me on the side of the road. Swapped that out and no problems since.
Make sure you check the gap of your plugs!
When my coil rail died and I found evidence of arc-through near one of mounting bolts.
See picture, that is what it looks like when the high voltage finds it's way to the mounting bolt washer
Usually because the plug gap is too big, X2 by the way.
if the resistance is too high, high voltage will always seek the easiest path to ground!
It could be that bolt, or even another set of internal coil wires.
I could see this sparking to ground when running engine at night.
Also, clean all the gunk off the rail now and then.
I cut large inner tube washers to compress over the metal bolt bushing and washer.
the miss stopped for about 3 minutes... then the inner tube washer caught on fire.
Look at mounting bolt areas in the dark and see if you see little flashes.