That clearance is pretty close, but I have some bikes with that much, or even less. Is the BB you're using the appropriate one for that crank?

I wouldn't worry about it unless your cranks/frame flexes so much that it hits your frame.

10 seed cassette should fit on a 9 speed hub. FWIW I am using 9 speed shimano cassette with a 9 speed campy group and it works fine, if you want to get the bike rolling sooner.

Nice build by the way. Do you have the stock fork for it?