The alternator wires running along the engine case and up to the frame to the regulator should be trapped behind a small retaining plate and screw that is just to the upper right of the pulley (as you look at the bike from the left side).  After that, they run up the frame and are held with reusable zip ties.  You should just be able to detach the wires at the regulator.

Sorry about the timing cover plug!  I've done the same thing.  It was a tiny chip that knocked off in there.  I just left it in there and hoped it wouldn't travel elsewhere.  I rode that bike another 1000 miles or so and never heard from it.  But, don't trust my stupid ways.  I'm the guy that breaks off dowel rods in the spark plug hole and into the cylinder!