Hi Dave, I've not experienced the change in AAU wobble when removing installing AAU center bolt. I lock them down well to set unit in taper before I remove bolt though. Yet not overtightening.
I verify bore of cam taper is smooth, burr free including peg. I verify the AAU taper is smooth, burr free. The AAU is often burred by poor alignment with peg during install. Easy to do.
I always feel peg as I install AAU so I know it's fully engaged. Then tightly hold AAU into taper keeping it straight as possible so taper isn't skewed even slightly or it might stay skewed. Then still holding I install bolt & tighten it. Only then do I let go of AAU with other hand.
Regarding Electronic ignition rotors. They have no taper. When installing you set motor to 38b with rotor mark or TDC tool. Then loosely install rotor. It must not touch pin at all!! If it should touch you need to file end of taper on rotor such it no longer touches pin.
With TriSpark you set pick up plate in place slots centered. There is a witness mark on pickup. Transfer mark to points cavity. Remove plate. Install rotor mark with the mark you just made & lock rotor in place. Reinstall pickup plate, start motor & strobe time.
you loosely install rotor. Install pick up plate slots centered. Pickup plate has hole drilled in it. The rotor has a white dot on it. Set motor to 38b. Spin rotor until dot shows exactly centered in the "window drilling". Lock rotor in place. Start motor, strobe time.
These are the only ones I have personal experience with, but others are similar.
Notice there is no provision for static timing as you'd have with points. The basic alignment of rotor is only close enough to get motor started for strobe timing.
Later timing covers are like a special tool for early bike owners. There are work arounds, but if you have the "tool" it makes life much simpler. A beat up junker will run you $40-50 eBay. Even junkers are in demand for this reason. Good ones with no damage will be $130-200. Make sure they have pointer & no damage in pointer area. Most damage is from foot peg hitting cover. Even still cracked on is fine for special tool use. Do not get repro, they are junk sand cast & don't fit right.
In the end of the day, I'd buy a later primary cover & use it all the time, or just get the cheapest junker from eBay or wherever & just use it to set timing. If you have allen head bolts at bottom of primary cover, with cut off allen wrench you can often remove cover without removing the exhaust pipe. With the right combination of tools & some practice removing foot peg is very easy. Hold up brake lever with bungee cord. Then back off the brake rod adjuster.
Thing is with EI once you set timing with strobe it really doesn't change at all. You'll forget about timing checks until you have to remove pick up plate for some other repair. Be sure you have the correct 70-4707 seal on wire to prevent moisture getting into points cavity. Very important even with EI.