Honda Repair: 99 Honda Misfire, spark plug wires, vacuum seals

Question
Hey
I have a 99 Accord(2.3 vtec auto). I changed the catalytic converter because it was making the engine run sluggish, then as i was driving away (from the auto shop) the car started to run really rough at low RPM's(idle-2800rpm) after 2800 RPM it runs fine. This only occurred right after the converter was replaced. I turned around and went right back to the mechanic. He said a tune up will fix it so I changed the spark plugs(replaced with ngk), spark plug wires, distributor cap, PCV, & new air filter, and also had a friend clean the air intake, but the car is still running rough. I also did an audible and a physical (touched all connections i could see, im no mechanic) test to check vacuum seals, and all seemed well. The Check engine light flashes and the diagnosis tool is giving me misfire codes. A mechanic I work with told me to pull the spark plug wires from the dis. cap and if the car runs worse then that wire is good, and if it doesnt effect it, its the bad wire... its the wire from cyl 3 but i have no idea where to go from here, as Ive replaced it already. I don't have the money for taking it to the shop but i was wondering if it is something simple. I'm totally lost on this an really need your help. Thanks

Answer
First of all if it happened right after you got it from the repair shop you need to be asking yourself if this is something that they messed up on. Sometimes these things happen just as a coincidence, but most of the time the shop messes up on something then won't admit it.
A flashing check engine light almost always means that there is a misfire. You have confirmed this by checking the codes. You should have had code P0303 if it was cylinder #3.
Some of the common things that cause misfire codes are spark plugs, wires, injectors, coils, etc. Go back through and make sure that all the wires are on the right plugs and that they are all on tight.
I would also go back to the shop and ask them if they screwed up. They would probably deny it anyway, but if they don't convince you or they treat you badly go to another shop.