98' civic 'Check Engine' light after header install

I did a search and it seems like this is a common problem after a header install. The header we put on eliminated the factory Cat. I followed the steps most people do to reset the ECU and the light stayed out for awhile. But sure enough, it came back on last night so I am thinking that maybe there is another problem with the car. We are going on a long road trip tomorrow so I wanted to get this straightened out before we go if I could.

I looked on http://www.hondata.com/techecucodes.html this site and it was very informative yet I had a couple of questions. The car is a 98' Civic LX, so would it have that 2-Pin diag connector that is to be shorted out to read the trouble codes from the check engine light? They didn't mention if this has to be done with the ignition on or off. Or would I have to read the blinking LED on the ECU itself? Any help is greatly appreciated! Thanks.