R&R front and rear wheel bearings. Check for swing arm looseness, if necessary install Kiegler mods, split ring shafts to stabilize the swing arm, check the swing arm bushings. Get a better headsteady, at least the later version, if not a heim or rose joint HS, this can be put off. Dave Taylor HS is reasonable. As Les says, gearbox layshaft bearing for sure. While you're in the gearbox, check all the sleeve bearings, especially the one to the sprocket, it is prone to drift out and get eaten up which makes for a loose/bent shaft, there's a fix for this. Make sure gearbox going through gears correctly. Check/adjust primary chain and clutch. New isolastics, Hemmings vernier adjuster, there are other options on the vernier adjuster. New tires/tubes of course. Open the timing case and check things in there. Have new rubber parts and gaskets to re-install, the slotted screws can be replaced with socket head 1/4-20's. Go over wiring with a fine tooth comb. Remove the blue capacitor, it's probably shorted or at least dead, you don't need that unless you're going to run without battery, just tape up the dead ends. Check alternator output, running at 2500rpm or more it should not completely discharge on your ammeter with headlamp on, but most likely will discharge to some degree. Pazon SureFire EI is reasonably cheap and effective, the AAU is most likely worn out. Rebuild the front end, new fork tubes and bushings, clean and new fork oil. Set up the front TLS brake properly, that brake can be made to work reasonably well, but will always fade with heavy braking, otherwise drag your feet. The front brake cable has a switch in it which is a disaster, consider getting rid of it and installing a different type switch for the front brake and a cable with no switch, no good options I know of here. New shocks, chain? I can go on and on. Lots of little upgrades that can be done later to make it a bit more reliable. I know nothing about that single carb. You should be able to do this over the winter.
Do me a favor and look up around the coils and you should see 2 pair of heavy red wires that will be connected together (4 wires into 2) to ground or earth. Where are those 2 double red wires connected?