Start with the ignition off. First, use the multimeter to check that your spark plug wires are good, and the coil outputs are good. You can test these individually with the multimeter - assuming that you have resistor caps in your plug wires, the resistance from the coil end of the wire out to the boot where the plug is inserted should give you somewhere aroun 1000 to 5000 ohms. (One can get plug caps of either 1000 or 5000 ohms, typically). The output coils of the various ignition coils vary in resistance, but usually these are in the 20,000 to 50,000 ohm range. If each plug wire checks out OK, one should also be able to put the multimeter leads on each plug wire boot and measure the total resistance, which should be somewhere between 22,000 and 60,000 ohms (depending on caps, coils, etc.). Write this number down, and then see if the bike will start and run.
Assuming it does run, bring your multimeter along with you and run it until you encounter the problem. When it happens, turn off the ignition key, dismount and quickly pull the plug wires from the sparkplugs and check the total resistance with your multimeter - you should get a number very close to the first number you measured. If the multimeter's number is alot higher, or reads as open circuit, then one, or both of the coils's secondaries are opening up due to heat.
The coil primaries should measure less than 5 ohms of resistance each, but you'll have to take the tank off to check them.
I *think* that the kill switch test will also work with the points-type ignition(?) At least, it is handy with the solid state ignition units - one takes a spark plug out and bungees it so the metal threaded section is held against the cylinder fins. (It helps to do this in a dark or shady place). Make sure the Kill switch is in the RUN position, and turn onthe ignition key, and, closely watching the sparkplug for it to emit 1 spark when you flip the Kill switch to STOP. You can repeat the process for the other cylinder. IF the spark occurs, then it is likely that Kill switch is OK and the coils and plug wires are OK, and the problem lies somewhere inthe bean can or the wiring to it. IF the spark doesn't occur, it could be a shorted Kill switch or problem in the coil(s) or plug wires.
someone correct me if I am wrong about the Kill switch/spark test with points ignitions - I think that it would still work unless there is a failure such as a short in the beancan (assuming good wires and coils), but all my airheads have been converted.
The voltage checks that Barry identifies above are also good and I'd recommend that you do perform those when testing in your garage to make sure things are right to begin with - though of course this means pulling the fuel tank off. You can wiggle the handlebars and some wires as well to see if the intermittent problem is a bad wire or connection. It isn't always so easy to pull the fuel tank off on the side of the road to measure those voltages, but if you can do so, great!
