You've had some good advice so far. I think profit depends on the area - here in the PNW 12% is pretty typical.
An important point is to find out what that includes - he will of course add taxes, but what about his "general conditions" like equipment rental, insurance, bonding, office overhead... make sure that he's including or at least itemizing these things for you.
Get a copy of his standard contract and have your lawyer look it over. It should include procedures for changes to the contract, including profit on those, and clauses for what happens if either of you chooses to terminate, etc. Before you sign a contract you should have a complete itemized list of costs included. Try (talking to neighbors or the city building department) to find people he's worked for that he may NOT give you as references.
You could insist that he get multiple bids from 2-3 plumbers and electricians, to make sure prices are fair, but he'll probably balk, saying he wants to use people he knows and trusts, and if you insist he'll get prices from others known to be high...
I always have my clients interview at least three contractors before choosing. Usually it comes down to a "gut feeling" about someone you can trust and feel comfortable with...
Who is designing this "custom home?" To me that means it's not just a house out of a plan book?? If so your architect or building designer should be guiding you through the contractor selection process...
I could go on and on, but I guess I just did.