ignition problems

I'm having trouble with what i think is the ignition, everytime i start it up when its cold outside it pops and bangs thru the exhaust and it sounds really muddy but it will smooth out once i get the rpms up a little bit, then when it warms up to operating tempature it almost completely goes away but my engine is idling pretty high and i have the idle on my carburetor turned all the way down, what could be causing this?
It's a 360 crate engine magnum in a 1991 dodge power ram, its carburetated fuel injection and computer are gone, the owner before me had the charging system wired up wrong, he had the blue wire coming from the voltage regultor tied into the primary side of the ballast resistor, i was told that blue wire needed to be tied into a 12v ignition source, so i tied it straight into my ecu power wire. Ever since i tied the blue wire from the voltage regulator i fried the original ignition module, i dont know if having the blue wire from VR tied into the ecu power wire caused the module to fail, or if it was already on its way out and failed do to the overcharging that was going on from the previous owner having it wired up wrong.
I am at a loss here.... i do not know what is causing it to run muddy and pop and pop and sputter out the exhaust, the two things that come to my mind first is the timing and then the coil, is it possible i fried the coil with the overcharging? is there a way i can test the coil to find out if it is still good on my own? how many volts should be at the coil while running and all that good stuff? when i timed it i timed it while the charging system was wired wrong because i was not aware of the overcharging problem, is it possible that what sounded good while the overcharging was going on is not working now that the charging system is working right?
I just dont know, timing and coil are the only two things i can think of that are causing this, distributer cap and rotor are brand new as well as the coil and the ignition module, any advice or opinions would be greatly appriciated.