Hey Mark, congrats on the new build. First, the true cost issue can (should) be solved by having multiple quotes by other builders and general contractors. Second, you can use a website called Homewyse dot com to see what true cost are in your local market (ie; materials, labor, etc). Also a book produced by the DEWALT tool company called Construction Estimating will give you the basic to feel confident at the pricing table.
After picking the best price quote for the project you'll have a number of different ways to structure the draw schedule. Set completion marks that need to be met in order to receive further draws (ie: completion of foundation draw 1, framing draw 2, ruff plumbing draw 3 etc). Or find estimated time scale for finish project and divide into even monthly payments. A draw schedule of five to seven payments is common for a new house.
Lastly, you can require the builder to have both a bid bond and performance bond before being awarded the contract. The bonds will require the builders insurance company guarantee repayment of project funds if he fails to meet contract terms (ie: complete the project).
Hope this helps, and I wish you and your wife the best of luck.