You are correct about not disconnecting a plug wire on any electronic ignition including the Dyna III. If done this way the box will die if not right away then pretty soon after. It is also not a good idea on even a /5 but a lot of riders get away with it I know.
You need the tool listed on this page about 1/4 of the page down. Called the BMW Airhead Carb. Sync. Adapters. Either buy these or make your own.
In operation the threaded rod is attached to the spark plug and the plug wire is attached to the other end. The bike will run in this fashion on both cylinders. Tighten the tool onto the plugs. It will come loose from vibration and cause the problem you were trying to avoid by using the tool. A long blade screwdriver is used to short the rod to ground, a cylinder fin, and the bike will run on the other cylinder. Instead of disconnecting a plug to keep it from firing we are now shorting the plug. Sometimes called the "shorting tool".
When done disconnect. I have personally learned to not leave these attached to my plugs and ride around too much. They will come loose, as I have already mentioned at least once. Good Luck.