Shifting issues

Hi, ill start from the beginning. My car (97 sunfire 2.4L Auto) died on me while it was in idle. Since then it wouldn't start. I checked the codes and received one which was to replace the Throttle Position sensor which i did but this didn't fix the problem but the code has disappeared since. I did however lose a screw and the one i used doesn't tighten it completely but it was the closest match home depot had. I then replaced the spark plugs and tested them, they were fine. I then narrowed the problem down to the fuel pump, replaced it and the car started just fine. Im not too sure about the returning two fuel lines from the fuel pump so they're is a 50/50 chance they're wrong. I took the car for a test drive and immediately noticed the car wasn't shifting. It would reach 6000rpm and beyond. It didn't even seem like it was trying to shift. Before the car died on me i didn't notice any shifting problems and therefore i dont beleive i have a bad transmission since i didn't touch anything under the hood besides the spark plugs and TP sensor. I checked the OBD II codes again and received the code P0405 which is EGR flow sensor A Circuit low input. I however do not have the slightest idea what this means, how to fix it or if this is my problem. I would greatly appreciate any suggestions and advice provided even if its a long shot.

Gavin