Idle and 3,000 rpm timing are not the same. The Yamaha ATU is famous for curious failures.
Most often you will see just fine idle timing but seriously over advanced run timing. Give it a good look.
Curious , I don't remember having to open points much more than .014-.015"" to get sufficient dwell ...
The following was written for a 4 cylinder but it is essentially the same .
Well the manual doesn't do a very good job of explaining this so ...
Set one set of points to the proper gap and place a dwell meter on that set of points and take down the reading .
(doesn't really matter what the number is or how many cylinders because you are going to make the other set the same . Just pick a setting that gives you a reading around mid scale)
Now get the bike running and set the other set of points to the same reading .
Ok now the almost kinda tricky part . Connect a timing light to the bike and moving the entire breaker plate assembly place the timing mark (usually for 1 & 4 ) within the 1/8" or so that is the full advance mark .
You will notice that one set of points is "usually" solidly connected to the breaker plate assembly (again usually 1&4 but not always ) and the other set (2&3) will move not only in advance and retard but in gap also .
Switch the timing light to 2&3 and again place the mark in the 1/8" that is full advance .
go back and check dwell for both 1&4 and 2&3 . if the dwell and the timing is reasonably the same for each set within a couple of degrees you are done .
Again it's important to not exceed the full advance mark.
Photo credit and hand model Stormie Ray .
(there are unusual cases) . If the timing does not retreat to "T" mark but to a retarded position your ATU needs a serious look.
Boy I'll say!
but you may need to adjust the size of the condensers to more closely match those coils.
And finally....
Testing Ignition Coil Wiring Reversal.
With the ignition off, engine off, pull a spark plug wire loose from a spark plug. Place it loosely back in place.
Now start the engine. Hold a no.2 lead pencil carefully in one hand. With the other hand, pull the loosened spark plug wire slowly away from the plug. You shoud see a good size spark jumping from the wire to the plug. Now... CAREFULLY place the sharpened lead point of the pencil into the path of the spark... you should see a "flare" of particles flying from the pencil lead TOWARDS the spark plug. If you see a "flare" of particles flying from the pencil lead TOWARDS the wire... you have the coil hooked up backwards. Remove the pencil lead from the spark path. Replace the wire. Shut the engine off, and re-reverse the coil low-tension wires and re-test. Get it right!
Why does this matter? If you got this wrong, you will be losing about 50% of your voltage at the spark plugs! Weak spark! Essentially, if the ignition low tension coil wiring is reversed, the coil will... "pull" spark, rather than... "push" the spark. Electrons prefer to leave a high-temperature (high energy) surface (like the center electrode of the spark plug) rather than a low-temperature (low energy) surface (like the arm of the spark plug). More voltage (more spark) is available if the electrons move in the correct direction, in the direction they prefer, from the high-temperature center electrode of the spark plug to the (relatively) low-temperature arm of the spark plug.
Oh yeah , I know I do this all the time but ,
Adjust the valves. If not gawd almighty will create another politician or kill a kitten.