1998 Jetta Acceleration Problems

I have a 1998 Jetta GL 5 speed.

I've had the car a few months and since I got it the acceleration and overall power of the car has been poor.

At low rpms the car runs fine but up around 3000rpm in any gear the car starts to shake and jerk back and forth. The check engine light usually stays off unless i approach 3000 rpm. Then the CEL starts to blink. I also have trouble maintaining speed over 40 mph. Even when I downshift there is virtually no power there.

I recently replaced the fuel filter and the O2 Oxygen Sensor (Pre-Cat)
The fuel delivery and exhaust systems seem to be fine so I feel like it is a computer problem.

Could the car be in "Limp Mode"? I've heard that a bad Mass Airflow Sensor (MAF) could cause this.

I'd appreciate any help. Thanks