I've heard the secret to getting contractors to do what you want is "Name a price, then do it." Basically for everything non-standard you want in the build, let them set a price, and then pay it. Oftentimes it'll be a few thousand for extra wiring or moving some outlet around, $25K to raise the roof in a room, something like that. But if they feel like they're getting an extra few grand out of you, many contractors are very willing to do it.

It does mean that costs frequently balloon, but you should expect that when you do any form of home renovation, and just budget an extra $100K or so for it.