Hugh,
 I had pretty much the same thing happen on my Kitfox with the older mid 
90's engine. The engine would quit on one" mag "  After a lot of wire 
switching,etc it ended up being a broken wire. 
 Check the red power wires to the A and B modules. (or whichever doesn't 
work) The way I did it was to get an ohmmeter and but one lead to a ground on 
the engine (engine is NOT running by the way) then get a sewing pin and work 
your way down the wire from the connection at the modules. Punch thru the 
plastic sheilding of the small red wire with the pin to make sure you have 
continuity in the wire.Do this about every couple of inches or so all the way 
to the back of the engine I would be willing to bet you will find a break in 
the underlying wire and it is just barely touching at the broken end thus 
causing the module to be intermittently powered.That was the case with mine 
AND the break was in a straight wire run making it totally invisable from the 
surface . I found the internal wire break just a few inches from the module 
connection. I cut the wire,spliced it ,and am now back in business !
 I hope that is your problem
                                         Dick Maddux
                                         912 UL
                                         Milton,Fl