Thanks again for the input, I'm sure that with this info I'll get it right soon.
Actually, I have been running the pipes for a while now, and am pretty satisified with them, with no popping or anything.
I put the carb on and tried to change to a velocity stack, but I didn't want to run without an air filter so that's when I found the restricted airflow using the foam velocity stack air cleaner. I switched back to the stock BD air filter, which has a K&N filter in it. Everything good at this point, ran like a scalded dog, so to speak. That's when I tried putting the Thunderheart ignition back on, and that's when I encountered the dead spot on acceleration. You're exactly right Jake, I did try to switch to the stack and cleaner and run the Thunderheart at the same time, but after changing back to the stock airfilter and ignition everything was jam up. I had a couple of cough's through the carb, but nothing that appeared serious. It was then that I decided to try the TH ignition again, and that's when the hesitation began. When I hit the throttle, it dies for a second, then catches back up. That also is what prompted the question about the ignition, because that's what I changed just prior to the hiccup. I do plan on getting the interface cable adapter tomorrow so I should be able to see the map, but I don't plan on changing it right away, just fixing the tach input because it's at half speed. That is, of course, unless you have some suggestions regarding the map, but trying to troubleshoot a map here would probably be like flying an airplane blindfolded from the back seat...
