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Q: Rough Idle, stalling at stoplights, random misfires at higher speeds...thoughts? on 2003 Mazda Protege

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!
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Just to clarify.... if it starts running bad , you can shut it off and then re-start it and it will run OK again for a while? And all you do is shut it off with the key and re-start it? Just confused with the "runs poorly until I shut it off and start it again"
Exactly. It's odd but when it starts stalling out I just pull over, turn it off for a minute, then start it up and go. It doesn't last too long until it starts having issues again (within a couple miles), but it's enough to get me to where I'm going.

As an update though, over the last few days the problem has gotten much better (no longer stalling, just hesitating at times when going to accelerate). Perhaps it really is just bad gas and I have to run it out of my tank before my engine runs right again.
I would retrieve any codes in the pcm first,but a cheap and easy way to diy is while engine is running run some water over the top of the engine and listen for the slurping noise and change in the idle,if it does this you've got a healthy vacuum leak,probably from the pcv tube.
Thanks for the suggestion! I do have a cat code that I have had on for over a year. We cleared it out last week, and it came on after about 200 miles.
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