It is possible to pinch the points wire between the cover and the engine when tightening the 2 front cover screws. Tightening the screws breaks through the insulation on the wire and shorts out the ignition system. That 1 wire needs to be positioned very, very carefully, "and you need to hold your mouth right" during the entire process. 

Even home mechanics who have replaced that cover hundreds of times can pinch that wire. 

If that's the issue and raw copper is left exposed on that wire, then you may need to add some heat shrink to make sure no contact is made when the cover is properly installed. 

Russell, Just want to reenforce what Richard said.  I've attached portions of instructions from MOTORRAD ELECTRIK for installing their Alpha ignition system.  Rick makes it pretty clear on where to route the wires from the bean can up to the voltage regulator.  I've experienced this issue in the past and the solution was rerouting the wires.  As Richard said check for bare wires and insulate them.

rick Schroeder #12173

81 R100RT

Russell,  I could'nt get both pics in the original reply, so i'm adding this to show what MOTORRAD ELECTRIK stresses.

good luck

redhorse 12173

There is no place to mount a physical restraint for the wire. But if you clean several spots on the inner case, a glob of silicone sealer can be used to route the wire and physically keep it out of harm's way.