Did you buy the parts and bring them to him? A good motor assemble-ing with dyno time can easily be 5k and up. Thats them just putting together what you brought them. it takes alot of time to be sure all the clearences are correct. if your using a reputable motor builder paying for his experiance and expertise comes at a premium, but it's worth it.
What compression ratio did you end up with? if you want to go more than 5psi in the future nows the time to make room (in the combustion chamber) but even 5psi makes lots of smiles.....enjoy it.