check the cont from your coil + to the ground. AND you may have to rip the entire harness out and find that the pipes burnt it in a spot and its a minor ground out. if you plugged in the new box and it doing the same thing may have fried that one too..
dyna's are more sensitive than a stocker. BUT a stocker CDI would surely have an issue if there was a grounding problem.
check the stator also.