Check your mag pickup polarity,it causes all sorts of problems if its reversed.we have found many MSD distributors with the magnet upside down reversing the polarity of the pickup.even if you plug the dist in with a msd plug it can be wrong. to check this unplug your dist and make up a pair of short wires.plug one end into the dist and cross the wires and plug them back into the loom. start your engine and see if the timing advanced or retarded. the correct polarity with an analog box is the most retarded position. with a digital box its the most advanced position.
also make sure the orange and black coil wires are not in the same loom or running parallel to the mag pickup wires. the 600 volts or in those leads will induction fire the box and cause all sorts of engine damage like piston or bearing failure on a engine with correct clearances and tune up.Bill