I did this yesterday. I completely forgot to take photos.. My wiring was UGLY. I've been re-doing most of it a little bit at a time and this project is definitely one of the items on my list. After I finished the Stator wires, I cleaned up the wiring for my Dyna system.. the area in front of the battery looks MUCH better now.
Next is the area aft of the battery.
The bike is essentially just another bike... The pilot is CRAZY.
Does the solder have to be clear flux?
What I have is 1/16th dia. 60/40 rosin core electrical repair solder, will this be ok or do I need to go find some that says clear flux on the label.
It might be too late for you but yes, any solder with non-acid flux core (such as rosin) is fine.
I highly recommend coating the wire with RTV silicone immediately before shrinking the heat shrink in order to absolutely guarantee that no moisture can get in.
An alternative to this that will allow you to still remove the engine without cutting the wires is to buy new contacts (or a whole new connector) from Eastern Beaver.