Those 40mm racing tyres are not suitable for commuting. A tough 28-32mm seems to be about right for all-weather commuting on rough roads.
Given the amount of clearance you need for these tyres (+ fenders), racing style caliper brakes are not deep enough, but you can get long drop calipers made for light-touring/sport bikes. I use these on an old style all-round road bike, and find they give better modulation (control) than the cantelever brakes on my touring bike, and the stopping power is every bit as good. The Shimano 105 version is recomended.

Cyclo cross gearing is often a low-ratio double (36/48) or sometimes a triple. Both are suitable for general purpose road riding, but you may want to customise the gearing to give exactly the ratios you need.

There are some production sport bike of sufficient quality, and you can also get some fairly good value frames which you build up. The advantage of a custom build is not that you use the very best components, but that you can put your money where it really counts (headset, bottom bracket, wheels), and use cheaper or even used components for bars/stem/post, and any other non-bearing part.

Soma do a sport frame for about $500.
http://www.somafab.com/extrasmoothie.html

You will have to check out the usual suspects at Bianchi, Trek, Jamis etc to see if they still do a sport model with long drop calipers. They seem to be switching to cantelevers in order to fit wider tyres for more touring capability.