I am looking for a little guidance on what to check next with regards to cylinder misfire diagnosis.

2013 R55 Cooper Clubman (justa). Engine bogged down badly on acceleration and was throwing misfire codes. There was oil in a couple of the sparkplug wells (leaky valve cover gasket) and the rubber boot on one coil pack was very degraded. Plugs needed replacement for sure.

So.. I've replaced the following:
All 4 sparkplugs
All 4 coil packs
New valve cover gasket
2 camshaft position sensors

After this I'm still having some trouble. On cold start the engine idles a little rough and will stutter a bit when trying to get into first gear. Then it'll throw the CEL.

Then here's what's strange -- If I clear the codes with my wifi connected OBD app, the engine will return to what sounds/feels like normal operation.

After the engine warms up, the idle is OK except for an occasional dip in revs every few seconds. I can drive without issue, but anything more than light acceleration will trigger the CEL again and slightly rougher operation.

My OBD device/app (Car Scanner) shows a "Permanent" (inactive) P0300/P0303 codes even when the CEL is cleared.
When the CEL comes on I get a P0303 (pending), and then 27BA, 27BD, 2781, 2775 codes.

Any suggestions on where I should focus further diagnostics?

I'm guessing fuel system - maybe a questionable injector?
Bad gas even? (I did add some fuel injector cleaner to the tank, but have not added fresh gas yet).

Thanks in advance!