nd22121

I was at the beach this past week and the one day was extremely hot. I went to start my 03 GT and it stuttered on startup and didn't start. I tried almost immediately after to start it up and it started up fine. I noticed the SES light came on and I read the codes and it was the P0340 that a lot of people seem to get and a P0300 which was a misfire code.
From what I've been reading, a lot of time it's the alternator. But I haven't seen people getting the misfire code at the same time. It seems to drive fun but to start it you have to get on the gas pretty hard and it smells like fuel as soon as it starts up.
I was going to flash my PCM back to the stock tune and take it to my mechanic and have him test the alternator.
Does anyone have any suggestions or opinions for me? The misfire code is what's worrying me since I havent read too many people getting that.

Thanks.