ECU Codes for 97 Integra

I tried to get my Integra smogged about 2 weeks ago and when they plugged in the test machine my check engine light came on. The codes it threw were a 71 and a 73 which are misfire in cylinder 1 and 3 respectively. I don't know a whole lot about cars so I took it in to the shop. They said to try changing rotor, cap and cables (the plugs had been changed about a month earlier). I swapped everything out and reset the ECU and everything appeared to be fine - the car was running great and no CEL. 2 days after I did the work, while driving, the CEL came back on. I've got about a week to resolve this as I have to register the car by the end of October and I'm looking for some expertise. Any ideas would be welcome....