I'm trying to find the manual for the shocks, there's rebound dampening adjust so....??  Already have the preload backed right off.
+1 on electrical issues.  With the custom harness, and new electronic bits just makes it not quite so straight forward.
The tach isn't reading right, but decided to do a basic charging check across the battery.  Bike started fine, warmed up and settled into idle, with just a new touch of ruffness (sync / timing / plugs?).  However, the results were not good. 

  off - 12.97V, ign on - 12.4V, idle - 12.3V, at well over 3K( 

) - 12.3V 

  Bad part, or bad connection, time will tell.