A frame-up build is a lot of fun, go for it. There are a lot of minor details that can bite you, and if you don't have a lot of expertise already then just expect to get bitten by them and spend a lot of time troubleshooting issues. But if you like doing that then you'll have a good time. if you just want to bolt parts on and have it work then it might not be so much fun.
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!