"Error" While Pulling Codes?

I went to the local O'Reilly Auto Parts store and asked the guy to pull the codes on my '94 GT because my car has an oscillating idle and feels like itr is cutting out at idle and everyday driving. He hooks up the Actron code scanner and it appears that it is going to receive the codes. It tries to "LINK" but it won't. It says "Error". The guy asked if I had an aftermarket chip in it because he has seen this happen before. I haven't done anything except put underdrive pulleys and BBK shorty headers on the car.

Aside from my surging/oscillating idle problem, I do have an exhaust leak.
IThe only modifications are BBK shorty headers that I put on back in 1995.

Has anyone else ever had this happen?

What might be causing my rough/choppy idle? O2 sensors, TPS, MAF, clogged cat's? I changed my IAC and my idle was stuck at 2300 rpm, so I put the old one back on. I even did the "relearn the computer" trick.

Does anyone have a clue as to what my problem(s) might be?