Don't go with the cheapest custom home builder, especially if there is great difference in price. Your home is likely to be your most important purchase, and you don't want to be cutting corners and using inferior materials. If the builder can offer cost saving that is terrific, but recommending poor quality to save money is not a good idea.
Plan on going to the construction site often. If you see something being done you don't understand, stop and ask questions. It is far easier to change things during construction rather than waiting until the whole house is completed.