Make sure that accelerator pump in the carb is working. This is a symptom that it's not getting the little extra boost of fuel off the mark. But even if you go hard open on the throttle, the carb won't be able to keep up with the sudden increase in vacuum. The Mikuni is a slug and you have to 'feel' your way into the power curve. Give my tune method a try (I know you are subject to Cali EPA crap) but you can always re-set it when it comes to inspection time. If you can get the ignition to follow a similar curve to the throttle butterflies opening, you'll unearth some useful midrange power and improve your highway cruising top speed.
Well done to you for persevering. It sucks when you keep hitting a wall and can't get around it. The biggest issue you had was the coil wiring and the distributor being out a tooth. It didn't help that a workshop couldn't even hook up the fuel lines properly and took a short cut just so it would run.
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