Mike,
You and I are at about the same spot - never a ground up build, always wanted to do it and wondering which way to go. I picked up the Sept issue of Street Rod Builder and they have two articles that are relevant - one on a low budget build of a '34 3 window, and another on a sweet '36 where the guy bought a buddy's car built in the 70's and used that as his platform. On the ground up build they are using a N&N Roller, and their budget is set at $35k - an eye opener for me, and on target with what the guys hear are telling you (and by coincidence, me) - plan on lots more time and money than the cost of the roller.
I am torn right now between the N&N Roller and buying an existing car in the area - think the already built car is the smart way to go, but concerned that whereever I go it's always, "OK, you bought Joe's car.", or "You have really changed Joe's car - liked it better before...." From what I have heard unless you go out of the area to buy the original builder's ID is firmly engrained in people's minds, which makes the ground up build attractive (for me). If you build start a scrapbook to record your source for everything from the roller with factory certificate of origin to receipts and notes for every component that might be thought to be stolen parts. Get references to salvage title numbers on any used parts from wrecking yards, like engine & tranny. Your state may be more lenient, but many (KS seems to be one of the worst) are getting really tough to register a new build, and then it is a 2008 Home Built, not a 1932 Ford.
Good luck in your decision process. If you decide to build take lots of pictures as you go and keep us in the loop!
Roger