IMO, custom building is not near as expensive as what it used to be.
In fact, when we did our research last year around this time - deciding on whether to buy an older home, new spec home or custom build - custom financially made sense. It was a no brainier from there.
In the end, when the market isn't so flooded - we could easily sell our house for about $25-35k more than what we paid our builder. I'm not just going off assessed value.
We used Allegro Custom Homes. (
link) We'd
highly recommend them to anyone looking to build. Not only were they able to beat prices from the spec home builders and the 2 custom builders we looked at, they're service was great and we could always get a hold of them.
Through the custom process you'll change your mind on things frequently. They understand and embrace that. Plus, they are Cyclone fans - which is nice.
While a process that can test your patience, it was a lot of fun.