Mine is 102mm(686cc). You'd probably be better off just boring .020 over stock(100.5mm)
Install an 11:1 piston but you'll need to check the squish. My Weisco required an extra base gasket to prevent the piston from slapping the head.
Do a valve job. Mine has +1 stainless only because my valve seats were in bad shape. The machinist (
http://www.kenzcycletech.com/) said there are OEM replacements that are good.
Matching/cleaning up the ports aren't that much extra labor if you already have it in the shop. Do it right the first time.
Choose which Megacycle cam you want. The X2 profile is supposed to be more than worthy, and it doesn't require a new HD spring set. The X4, which is in my bike, gives you more middle and top end but requires the upgraded valve springs and checking for valve clearances with clay. You'll have to degree the cam either way if you are building the engine.
Don't forget to address the decomp
New cam chain too
Stock carbs rejetted and have that Tunebike/Off The Road carb kit installed on the CV side. I'm really surprised at how much better these carbs feel after 40 hours of tuning(yes, I'm learning as I go) but I still lose ignition up above the 7500rpm area and am telling myself that these carbs just won't flow enough consistent fuel air/mixture above the 60hp barrier. I'm ordering Mikuni TM34 B-65 carbs soon.
I have Projection Components headers as well but I don't think you need them to get a good running engine.