Leave the mixture screws one turn out. If the carbs are a little rich right now it's fine. The bike will run with the carbs set twice as rich as needed. Too lean will cause problems.
The bike will idle too slow when just started for maybe 10 minutes. It's this time you have to keep it running with the enrichners or the throttle. We balance to carbs for running when they get warmed up but they won't run the same when still cold.
Yes, suspect the flywheel is not mounted correctly. Must check. Wooden dowel or bamboo skewer.
It's also possible the advance unit is not returning to idle and this is causing the engine to race and be too far advanced.
You need to use the timing light to check advance at 2,500, 3,000 rpm. And verify the timing is going back to idle when the idle comes down. I think you did buy a timing light. But I suspect you have been setting timing with the trouble light at idle since you learned that trick. You have to learn a few more tricks to get this thing right.
The red light for the charging system will come on at idle. It is normal for the red light to be on when the engine is at idle. It will go off at about 1300 or 1500 rpm. That's normal. It is not a problem for the red light to be on when sitting in traffic. A good battery has enough electricity to run the system for quite awhile with the red light on. And then the battery gets recharged when you raise the rpm.
The yellow light for oil pressure should not come on at idle. It should never be on if the engine is running. The yellow light should not flicker when at idle.
From the settings given for the carbs only small adjustments should be made.
When trying to balance carbs the engine should not be over heated. If the pipes get red hot turn the engine off and let it cool. If you have a big box fan place it in front of the engine when balancing the carbs to prevent this problem.
I have to go to work now. Good Luck. Just think. only a couple of days ago this thing would not start or run or anything. Now it can go around the block. Progress.