i know of the shop, but dont know much about them.
its weird not to have any tell tale marks, when you go to rebuild, id deff get the crank checked out tho, trued and welded.
with the overheating, have you checked the water pump impeller, radiator maybe blocked ?.
running rich can cause overheating. does sound like youre rich, id play with jetting a bit. warm the bike up on old plugs and go for a bit of a thrash on new plugs, with out being off the throttle much. pull over and check out the plugs. they shouldnt get too dark straight away, a nice tan to lightish choc brown is good.
when i was running 280 mains 25 pilots with t5's, the airbox lid was on, but the box had 12 1" holes in it, running pods or without lid would prolly jet close to around 310ish.
my ported 350 ran 330's with t5's and that was jetted pretty dam perfect.
was piston to bore clearance checked out ?