I have a 98 Civic Dx, and today I was out driving around and I stopped at a gas station to get a drink left the car running in neutral and pulled the E-Brake while I went inside. When I came outside and got in the car, I released the E-Brake and pushed the clutch in and shifted to first, but when I went to depress the clutch and start on the gas I was doing about 5mph and my car was just puttering, same thing happened again for a couple more stops, then out of nowhere just stopped, and I didn't have any more problems on the way home. What could this be?

 

That is a PGMFI issue, not a transmission. Your question will be better answered in the 92-00 Civic section.

 

Your ebrake was still on despite dropping the lever, check your cable for seizing. you should have felt the car bog down completely though as you pulled away