I've spent some time verifying the settings on nearly everything for the engine. I also adjusted the compression on the rocker bolts for the front end.
First off, VM29 carbs don't have vacuum ports for synchronization so I added some. After the vacuum sync, the off-idle stumble is gone, idle is much smoother, and the throttle response is more crisp. A well synced set of carbs is paramount.
The plug gap was increased from .026 to .036. This made a huge difference in the heat of the plugs. They're running much cleaner and the exhaust note sounds a lot sharper. I'm going to bump up to .040-.045 soon. There is plenty of spark energy to cross a bigger gap. The plugs should take the heat too. The resistor plugs have helped with noise in the Tachometer signal and should also help develop more spark duration. I am planning on testing out some 10 kohm Resistor caps to increase the spark duration. The duration on a dyna spark is about 0.9 ms. The stock points system had a duration of 1.5 ms and the cb operates best with a minimum duration of 1.0 ms according to the wisdom of Hondaman. With the addition of a 10 kohm cap, I can run non resistor plugs and increase the spark duration by 15-20%.
I also verified the ignition timing and found that 1/4 was set to 39* and 2/3 was at 40*. Not a huge difference but certainly not good. I also noticed that the screws for the 1/4 pickup weren't very tight. After some thought, I decided to reduce full advance back to around stock so it's now set at 35*. I changed the timing curve to setting 5 on the Dyna 2000 which moved full advance up to 6500 rpm from 3500 rpm. When riding the bike after these changes, I noticed that the bike would load up easier at lower rpms. I think this might be due to the lack of timing advance below 6500 rpm so I switched the the timing curve back to curve 4. This curve has full advance coming in at 3500 rpm. More like stock, which works well for many differently built engines.
All in all, cleaning up the timing, opening up the spark gap, and synchronizing the carbs has made a significant difference in the behavior of the engine. It has a much smoother idle, easier start, smoother transition off-idle, and a crisp throttle throughout. The suspension adjustments have allowed the front girder to move easier and I'm running a lighter pressure in the air shocks. I will post an update after I do some testing to optimize the spark gap.
I also lubed up the cables and affixed the speedo pickup to the rear stay to reference the rotation of the rear sprocket. Road tests were done with a temporary fuel tank and no rear fender since the originals are out for paint. A bit awkward...and a bit illegal.