I assume I just tie up the wires from the old harness going to both coils since the new wires go directly to the new ignition control unit from the coil.
The one question I had was about syncing the carbs the way I have for years by taking the spark plug lead off the plug as it's running to isolate each carb for adjustment. Will doing this with the fancy electronic ignition torch the electrics?
Hopefully the instructions dealt with the fact that the old twin coils on your 79 are of the 6 volt persuasion. IIRC, its been a while, there is a 12v feed and the original coils are wired in series and grounded through the points. Therefore there should not be any "spare" wiring left after removing the old coils, other than perhaps the points trigger wire.
As regards your other question, I don't see that removing one plug lead for a short period of time would harm anything, but if you are worries why not plug it into an old plug and ground that to the frame?
My real question is that I don't think much of your method of synching the carbs. Given that a highly accurate vacuum gauge can be made with a couple of sticks of timber and $5 of transparent plastic tubing which allows both accurate and more importantly fast idle synch (which I guess is what you are setting up) why follow a methodology that is tedious and time consuming?
In fact, if you want to look professional, find another list member and buy a set of Chinese 4 cylinder vacuum gauges and cut them down the middle and have 2 each (but i still prefer the plastic tube Manometer option because it is the most accurate).
