Rusty, we always knew you were "actually more mental" but i love what you're doing with that motor. I went to an italian republic day meeting on the weekend and IMHO a 650 engine looks wrong in the back of a 500.
If the combustion chamber is smaller than the bore I would leave it alone as you want to retain as much metal as you can in the head, especially the 499 thats had port work done. You cant really change the shape of the chamber in that head and the smaller the area covering the bore, the greater the force will be exerted on the piston, if that makes sense. I once mucked around with chambers and created hot spots everywhere. When it comes to modifying heads " a little means alot and alot can mean very little" as in a junked head. Just my thoughts....
As for comp ratio, I suppose you can always pull the head off again and stick a copper gasket under it, but a 5 minute math exersize gives you great peace of mind.
Oh yeah, before i forget, if you have the head apart, get a three angle jobbie on the inlet valves. You'll thank yourself in spades if you do, especially on those engines.