As I mentioned before pull your clutch cover and check the 3 timing marks to make sure your counter balancer is properly aligned. The tip of the crank on the right side has a punch mark that you also align with the crank gear when you install that. Then the counter balancer itself is scribed with a line which should line up with marker cast into the case. I'm now thinking that on my first assemly effort I had the crank gear installed with it's punch mark off from the actual crank shaft punch mark which is really what matters. Point is, you line up the crank gear so it's on the proper spline to make both the crank punch marks the same, then you work with the position of the counterbalancer gear until it is also lines up...
If you have to pull the crank nut off you can stick a penny into the gears to jam it so you can loosen it. The penny will mash and bend, but it doesn't hurt the gears at all. That way you aren't putting torque across the crank halves (like by holding the flywheel) which possibly could thow it all out of true. That said, someone could have held the crank with a questionable method in the past and thrown it out when removing or installing the crank gear nut to change the seals. A fixable issue if that is the case, but it requires a case split.
That said when I had my crank checked it was within 1/4 of .001" off, so it was darn near perfect barely making the dial indicator wiggle and was very much within proper specs.
Cool that you made some progress with the headlight. Mine isn't great but it's been good enough. It does dwindle to a dim glow at idle, but reved up it's pretty decent though when I ride at night with other riders I tend to follow the ones with nice modern lights!
I did get out on the Trace last Tuesday night, had the bike up to 55 mph that evening though it took a full tuck and a mild hill to get there. (edited)