"The crank arm is hitting the chainstay."

Maybe the arm has been pulled on too much, or has the wrong spindle.

"I can't slide a wheel in the drop out with a 126 or 130 spaced wheel."

Maybe its only 120.

"Can I safely assume that the frame could be properly aligned and coldset by a professional builder?"

Probably; a builder or a good bike store with an alignment table.