2009 Chevrolet Cobalt making me crazy

Hi, I have a Cobalt 2009 LT 2.2 with 94,000 miles on it.
Never a problem, regular maintenance and checkups since we got it on oct.2010. Fuel Pump died, took it to dealership and was cover under power-train warranty. Happy with that! -
Chevy dealer just took my word and didn't performed a full diagnosis on the computer, they just went ahead and replaced the pump ( not professional work right there)They had it for two days and when I pick it up an hour later check engine and service traction lights showed up like a Christmas tree.
Went back and claimed my issue which was never there before they took it to get fixed. They didn't believe me and wanted to charge for 2nd diagnosis which they never performed at the first time like I mentioned. The said nothing was wrong with the car and both lights mysteriously vanished. (Lights don't go off unless cleared by computer)
I said that and they changed the subject saying the technician drove it for 3 miles and nothing. (B.S)
The car definitely has a misfire (P0300) which we know is random.
They say they saw that but couldn't find exactly where it was coming from. (So, you tell me nothing is wrong with the car, then, Engine light vanished and then, we saw a misfire but can't really detect where), such a great professional technicians. Uh?
The car def. Has issues, sometimes runs perfect and you stop at a light and shakes like running in 3 Cyl, sometimes it doesn't. If you running on the highway sometimes is Ok till you push that pedal a bit stronger and the car struggles to accelerate normal and the engine lights shows up blinking with the service traction light at the same time and you take your foot off pedal and mysteriously goes away.
I personally researched and made a list to check and narrow down the possibilities. (Spark Plugs Checked and replaced, they were ok) Coils, working perfectly - Air intake residues? - Clean as new - Throttle bod - Clean - *Vapor canister purge solenoid - Not checked yet - *Icm - Not checked yet* - Clogged (Maybe) overheated cata converter - Not checked yet - *MAF - Not checked yet - Fuel filter clogged? - Not checked yet.

There is many things that I couldn't get checked yet, and that is why I'm asking for recommendations to narrow it down if it is a common issue.
My main big issue is that the car never ever had any lights on dash - issues before, always run really good.

Thanks and I really appreciate all the info - Help!
Have a Great Day!