There is plenty of help online to work through whatever issues come up.
I would start by talking with the frame maker or others that have built bikes on the same or similar frame (maybe there'sa forum for them) for component recommendations. Frame geometries and such can impact what components you can use.
I agree than the Zinn books are good - road bike or mountain bike, whichever is appropriate for your frame.
The build kits sound like a good idea potentially as long as you can get what you want, or most of it, in one of the kits. Components are really expensive when you buy them one at a time.
Obviously start by picking the big buckets you want to be in (disc vs cantilever etc. brakes, internal geared hub vs. derailleur, grip vs. STI shifters, etc) then work down from there.
Lots of great help online, good luck!