bypassing ballast with stock ignition module

because im running a 12 volt coil and if im not mistaken the ballast cuts down the voltage to 6 volts because the stock coil is a 6 volt coil.
Not really, it is a coiled design to work from 12 WITH the proper value of ballast. The actual coil voltage will depend on the ballast value (which changes with load) and the RPM some a lesser degree, and can be a lot higher than 6 volts.

One thing not yest discussed is if you have the right ballast IF you have a 4 pin ECU. There are a lot of different ballast resistors out there and only 1-2 are right for the Mopar system. The wrong one can kill spark energy and cause your symptoms.