1.The clutch switch...I drilled a hole in the underside of the bar for the wire to plug into the clutch. I left about 2-3" of the gray wire shroud on the wire. I tried to put a piece of braided wire over it, but it was just too small of an area to work with. It's underneath & hardly noticeable.

On the throttle side, I used another piece of braided plumbing wire. On one end it's concealed in the switch housing. At the other end I terminated it with a small clear zip tie...again, barely noticeable.
 

2.) The braided plumbing line that I ran the wires through goes through the triple tree & up into the handlebars about 3". On the other end, it disappears behind the neck covers. All I did was wrap the braided ends well with electrical tape to prevent unraveling.

3.) I drilled 7/16" holes through the triple tree.