[240racer]

can you tell why the ignition wires melted?  Do you think they melted because of something like hot water or oil getting on them, or does it look like they overheated themselves and burned up.  If they overheated, then something caused them to short.  Can you pull out the spark plugs and check them out.  Look for discoloration and stuff.  The small amount of smoke sounds like it was only the wires burning.  Did it smell like an electrical fire, plastic burning?  I would look into the electrical side first, from the clues you gave.  Check out the coil and other things, I think it would be unrelated to alternator and battery.  you said that you replaced the charging system, that doesn't include ignition wires, they are sometimes called spark plug wires.  I would look at the ignition system, coil, igniter or whatever.
Adam