Rough Idle, stalling at stoplights, random misfires at higher speeds...thoughts?

What is your question?

My car just started having issues a couple days ago when driving. It starts and runs good for several miles until it warms up and begins having idling issues/misfires while driving. It has gotten to the point that I throw it to neutral and rev the engine at lights to keep it from stalling. I've had one ignition coil replaced and put some octane booster into the gas, but it's still having issues. I noticed that I can hear something different about the engine before it starts having these issues. Almost sounds like something is flapping between open/closed, and once I hear it, it runs poorly until I shut it off and start again. Should I replace the other coil, or look into the EGR Valve? I really don't know a lot about cars, so any help with this would be great. Thanks!