Good luck with the rebuild, Harry. Remeber the quotes "Joseph Lucas -Prince of Darkness" and "The reason the Brits drink warm beer is that they all have Lucas refrigerators".
After 18 months at Norton (development and test engineer on the Commando and the AJS Stormer moto-cross bike), I would strongly recommend a total re-wiring and replacing as much of the original electrical system with things made by modern manufacturers.
I tried very hard to get Bosch and Wipac electrical equipment on the Commando, but was shot down on the basis that "the marketplace expects Lucas". After owning a couple of Renault cars in the US, I'm sure glad I didn't push for Ducellier or Paris-Rhone.
The only other change I think is essential in today's traffic is front disc brakes. There are quite a few after-market options, on which I wouldn't offer an opinion, but the original (Campagnolo?) twin-leading-shoe front brake was a real disaster. When you really reefed on the brake lever. the last 30 percent of the effort went into distorting the brake back-plate and didn't do anything for braking performance. I did some brittle-laquer tests to see what was going on, as the TLS brakes should have been much better that those on the Atlas, but were actually not as good.
Those original brakes didn't generate enough force into the frame to cause any problems, but I understand that better brakes will actually cause distortion of the two down-tubes. There's a frame mod to put a stiffener between the tubes to prevent the problem.
As long as you get the Isolastics set up properly, you'll be amazed at the handling and the lack of vibration. By comparison the Harleys handle as though they have a great big hinge in the middle of the frame and the vibration is significant. I've ridden several new-ish H-Ds and I'm not impressed, except for the basic "grunt" from an engine that big.
Of course the Atlas had a major problem with vibration. We reckoned a headlamp bulb wouldn't last much past 5000 miles, and it didn't matter whether it was switched on. The vibration would shake the filament off its posts inside the bulb! I rode Atlases and 650SS bikes a lot, and about 150 miles was enough for you to lose the feeling in your fingers and toes.
As far as I'm concerned, a bike that's too heavy for the rider to pick up if he falls off isn't a true motorcycle. Having to get a tow truck to pick it up for you is just not acceptable. The Commando prototypes weighed in at less than 450 pounds. the average Hog is about double that.
Good luck with the reconstruction and I hope you have many pleasant hours of Commando riding.