I had a bunch of misfiring nonsense that acted about like yours.. when the car got hotter it started misfiring bad.

I tried everything, MAF cleaning, plugs, plug coils, fuel filter, CAI or tune, etc.

Turns out it was a bad fuel injector. Car had 45k on it.

With the car running pop the hood and walk around and pull the plug wires one at a time and reattach them.
You should notice a drop in rpms each time you disconnect a plug wire. If you get to a cylinder that you cant hear a drop in rpms, you have a bad injector (or plug) on that cylinder. Reasoning is that the cylinder is dead already so nothing happens worse when you pull the wire off the coil pack.
Helps to have someone in the car watching the tach to verify what youre hearing. Do this when hte car is hot and misfiring.

If this is it, the good news is that for stock injectors its a 15 minute / $50 job. Good luck.