Depending on how neat you want it to look, it may be helpful to build a little mold or dam out of fish paper or stiff cardboard or poster board inside the alternator area. Line it with wax paper, and position it so you have enough to fill in the hole, and a little more. Put the alternator cover back on, route the wires, and pour in black silicone. Wait 24 hours or more. Remove cover, and peel back the mold and paper.
Denatured alcohol is probably your best bet for cleaning the wires. Simple Green may work as well, but I don't recall if it leaves any residue behind.
Thanks for calling the Permatex people. Good customer service on their part.
Luke M
Used to have a 1979 CB750L, sold it as a parts bike, now riding a slightly modified 1984 VT700C. Network/Field Engineer. Central OH, USA, Earth, Sol System, Milky Way Galaxy, Universe.