$410 is a lot to pay for a wheelset with joytech hubs and ok rims. I assume the "wheel build" price includes spokes?

You can get the extremely well thought-of Mavic Ellipse for around that (probably a few bucks more).
http://www.biketiresdirect.com/produ...track-wheelset

Then if you're worried about buying online, pay $25 to have them tensioned/trued at the shop.
Of course they'll probably not want to be your friend as much if you buy a superior product online at less than what they quoted. But that's how it goes.

Otherwise, without brands and models on any of your other parts it's impossible to know if they're screwing you.
For example: You cranks are Sugino? Great. If they're Sugino RD, then $110 is a fine price. If they're Sugino XD, then you're getting fleeced.