There are SO many different ways to go.
I have a custom built on a SA Milspec, several Colts that have been customized, an SVI hicap .40, and a STI open gun on the way. Also owned a series 1 Kimber.
Based on my experience, I would not build on another milspec. I'd use either a Capian or a new series 70 Colt. You'll be much happier with the end result.
A Kimber (full of MIM parts) will probably do just fine, but avoid the internal extractor and the series 2 safety system - too many problems with them. That leave the 25th anniversary edition or Hilton Yam's limited run of Kimbers, unless you want a Warrior.
A new series 80 Colt is an excellent base for a custom gun, whether just a few mods, or the full meal deal. Great looking rollmark on the slide, comparitively few MIM parts.
For an out-of-the-box gun, you can't go wrong with Baer and Rock River. If you can afford it, Brown.
Wilson builds a great product, but IMO they are between the high-end Kimbers and the Baer/Rock River/Brown guns.
Check out
http://www.yostbonitz.com/
http://www.rogersprecision.com/
http://signaturegrade.com/