Q: Car turns over but won't start and when it does start, it doesn't run correctly

I have a 2001 VW Beetle 2.0. The check engine light is on and the codes it read were secondary air injector incorrect flow and main catalyst efficiency below threshold. The other day I went to start my car and it would not start. It was turning over but not starting. I finaly got it to start after about 30 tries but the car only made it a couple of miles or less before I had to pull over and get towed because it felt as if the car was trying to stall every time I'd press the gas. I'm not sure if this is due to one of the things wrong on the check engine codes or because of something with the fuel so today I replaced the air filter and the fuel filter. The car is still doing the same thing as what I mentioned in the beginning, turning over but not starting. Should I try replacing the fuel filter or do you think my problem is one or both of the two codes from the check engine light?

My car has 97000 miles.
My car has a manual transmission.