Newbie: Just Bought My First Stang But Need Help!

So I bought a 2008 mustang gt premium on thursday, feb 20th. I test drove it for over 45 mins on the freeway and also through normal daily stop and go traffic and it drove wonderfully. Had about $10 worth of gas in it. So I buy the car and fill it up with 87 regular gas and drive home(25 miles) and runs great. Park it for an hour because of a storm that came through then go to start it and cel comes on. No symptoms so far. Take to autozone and the codes read P0171, P0174, P2195, P2197. I drive about 5 more miles and it starts acting up...like its not getting enough gas. Turn it off for a little while, starts back up and its running good. Drive several more miles, run it slightly hard a couple of times and continues to run fine with the cel still on. Let it sit for 2 hours and starts driving bad again. Basically sometimes it drives great and sometimes it doesn't. I changed the fuel filter and also cleaned the MAF sensor. Here's what I know about the car and what I was told from the dealership I bought it from. Has a C&L CAI, an off road(only has front cats) Hpipe. I know it did have a bama tune before the dealership got the car. They said they took it to ford to reset it to factory settings...not 100% sure I believe them. There could be other mods that I'm unaware of. So I'm thinking its one of two things. Since it supposedly is tuned back to stock, it's messing up because the cats are gone?(besides the front two). Or do you guys think it could still have the bama tune and possibly be set for 93octane fuel instead of the 87 I put in it? What would make it drive great for 45 mins and then after filling it up and 50 miles later start acting up? Any help would be awesome! I really like this car, just need it to run correctly.
 
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Well I know there were some issues with the cars and CAI's. Is it the stock MAF? Something is getting warm and acting up... and it could be an air temp sensor. Something on there is not liking the stock tune. The exhaust is not the issue IMO.

Find a way to get the stock air box on there to narrow that down. CNL states that there are diff configurations for a tune and no tune... Im saying missing the tune is the problem. It's a guess but a good one till you narrow that down. I bet you can find a stock air box setup on the cheap.
 
My 2008 has had 0 issues. its almost at 60k miles and I started using 89 and my car feels better and im getting better mpg. enough to know im saving 25 cents every fill up if I only do streets. more if I do highway. and I also have an aftermarket CAI
 
If they did in fact remove the tune, you may need another tune or put the car back to stock parts as mentioned. A tune may have changed the cat settings also. I would not drive it to much until you sort out the issues.....or return to the dealer and have them sort it out. They should fix it for nothing.
 
Most aftermarket CAI have a tune that can be purchase with them. See if you can determine what type it is and see if the tune for it is still available. They're usually pretty reasonable. I know that installing them without the tune can sometimes lead to issues. If not, like mentioned above, put the stock air box back in it and see what it does.
 
They have an aftermarket CAI and then they put back the stock tune - there is ur problem right there! get a stock airbox/air filter, also I would try to get stock exhaust back.