What brand gaskets have you been using?
I happen to have my local machine shop's price list right here - getting ready to get my 836 kit in my 750...
He gets $42.50 (+ $0.09 per .001") to remove material from a head. I'm not sure if he uses his milling machine or surface grinder. Lists $50.00 for deck surface clean up. You'd have to find someone in your area to see what their skills are and if you feel comfortable with them porting / polishing on your cylinder head. You should be able to keep your valves as they are, they might need a refacing and/ or new seals. MRieck is the local porting guru on SOHC4, many on the site rave about his work.
Most polishing (exhaust side only) can be done at home with a dremel tool. Matching ports can be a small increase in power and also done at home. Porting, really getting in there and removing material, can actually be more detrimental than helpful without having seen what the changes will make on a flowbench. On 2 valve Ducati heads I actually added material to the bottom of the intake ports and made 7+ HP 10+ Ft lb tourqe.
Paulages built an astonishing 550 / 650 hybrid. Track down his build thread, theres a ton of info there. I recall reading a stock 650 head will flow better than a ported / polished 550 head, but then again my memory ain't what it used to be!
If you go the decking route I have no idea what amount is safe to remove. I'd like to get an idea for my 750 engine, too. Whenever material is removed from this area the valve to piston clearance must be checked, usually with clay on the top of the pistons.
Good luck!