Blinking Check Engine Light
First time posting, hopefully I can find some help.
Two weeks ago the alternator went on my 2000 Maxima GLE. I replaced the alternator (fun). Immediately following the swap out the car began to run rough, the whole accelaration wall at 3500 RPM, bog at start, whole nine yards. After searching the internet found out the problem might be the MAF. So replaced the MAF and rather than take it to a dealership to have the ECM updated I tried the disconnect the battery and tap the brake for a half an hour trick, hoping that would work. Well drove around for a couple of days and the car had tons of new power felt like a new car. Did notice a fuel smell once the car was sitting in the garage after driving. Then a few days ago the CEL started blinking periodically. Again after looking the internet for a solution found some sites that said this is very bad and could potentially ruin the cat converter (don't want to have to replace that). So when the CEL isn't blinking it is on. Pulled the codes tonight and got 0301 cyl. one misfire, 1320 ignition system and 1126 thermostat.
My question is can any of the pulled codes be related to the new MAF that didn't have the updated ECM or are all these new issues. Mind you the car didn't run rough (bog down) before the alternator went. Any help or insight would be greatly appreciated.
Thanks in advance.