So I recently got my car straight piped I have long tube header x pipe and its straight piped through the back so the other day my car started hesitating and shaking real bad this morning i had cel and codes p0022 p0345 and p0349 so i changed my camshaft position sensor because that was one of the codes and did an oil change i cleared the codes with my sctx4 tuner drove fine then a lil while later it started hesitating and shaking again but then when i rev it up or accelerate it stops and I need help to figure out whats causing this problem i reflashed my ecu with my tune and thought that was the problem but still same problem

 

You might need a better tune. Or it could be the alternator is going bad. What year is your car? 05-09 the alternator can go bad but not show any charging symptoms.

Diodes fail in the stator which may not affect charging but throw a ton of electrical noise into the wiring harness which interferes with the Cam shaft signals. This will throw one or both of the P034x codes above and can cause the car to run bad from he crappy signals.

Sometimes a bench test will show an alternator that's failed this way but most of the time you need to have the electrical sine-wave tested with an oscilloscope. There is also the Parts Cannon but, I am not liable if you choose to blindly replace the alternator and it does not fix your problem.
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I’ve replaced my battery and alternator but i took it to the dealership and they said something about the timing degree off and it worn a bearing and I need a new engine so hopefully my warranty company cover it

 

Don't know what bearing they're talking about but a timing issue is possible if a Cam Phaser is failing. This would account for the P0022 code. To inspect the cam phaser you can take off the valve covers, set the timing to TDC and check that the cam phaser marks are properly aligned. You could even go so far as to remove the cam phasers and verify the aren't gummed up/broken. If you're going to go that far though, may as well replace them in the process as preventative. BTW don't buy aftermarket phasers, they are crap and will fail sooner vs later.

 

The dealership i took it to say its the crankshaft bearing worn but they claim my warranty wont cover but im taking it to dealership I purchased it from because I bought the car as is with all the modifications and the dealership its at say thats why my warranty wont cover which I think its stupid but im going to have the other dealership look at it

 

Really? Sounds to me that they're talking out of their asses.
Your car has LT headers and is catless. Has the tune been adjusted to delay the changeover to closed loop operation following a cold start and switch off the downstream O2 sensors. If not, your engine may be running lean for a short while after the ECU has gone from open to closed loop operation because the upstream O2 sensors haven't sufficiently warmed up since they're further away from the engine.
Cam position sensor codes are most commonly caused either by a bad alternator diode allowing a small AC current to leak into the wiring harness, or a clogged VCT solenoid restricting oil flow to the cam phaser reluctor wheel. It's rare for the cam position sensor itself to fail, and you won't get a fault code from a bad cam phaser unless it's bad enough to be knocking noticeably.

 

Dino im not really sure what the problem is like when it warm and I drive it I guess its a knocking noise I dont really know but when I rev it up or accelerate it goes away so im in the process of going to another dealer to look at it I think it’s a money scam because the car never been to that dealership but when I pick it up tomorrow I’ll record a video and post it so someone can hear the noise

 

Post a video of the engine idling with the hood open and the camera moving around it.

 

Mmm...Rod knock would be a "worn crankshaft bearing" aka "rod bearing"

Yes, get a vid with audio as Dino Dino suggested when you get a chance. Rod knock would present at the bottom of the engine and easily heard from the oil pan and not nearly as well from the topside/valve covers.