well I just figured my cc the way they do it in the (real world) I came up with 187cc total, I think it runs strong for such a little motor, 2mil stroker crank, .020 over bore.
probably silicone, that stuff is a no no.
if you feel the need to use any sealant on gaskets, use coppercoat spray.
like stated earlier use yamabond for the cases.
use some grease on the seal lips.
I would do resistance checks on the coil and stator and rule them out first, don't just want to through parts at it.
and if you just changed the harness check and clean grounds, and conections.
sounds like you had an air pocket in the cooling system, with that bad cap and just water it got hot and boiledover. a waterpump won't move an air bubble, so the water just boiled.
I live in michigan, and have used fast racing , and hjr, both are great to deal with. being that close to Kevin @hjr I would use him if I was you.
do it once do it right. call kevin.
unbolt the caliper put a block between the pads, raise the caliper above the master cyl. so the air bubble can rise to the bleeder screw.
also make sure you don't have the rod adjusted to tight, so the fill hole in the master is fully open.