I think we could banter all day about what is the best bike, but truth is for $3,000 you will have a lot to choose from. There really is no best bike, just the bike that suits you best. And to find that out, you have to go out and ride a lot of them.
I ride a Cannondale Carbon Synapse and love it. The Specialized Roubaix was actually too dampened for me and wasn't very responsive. I was enamored with it on paper but I hated it on the road. Other people love them. My husband has been really happy with his Wilier Izoard (Ultegra). To each their own.
Maybe an aluminum frame with a bit of carbon might be an option. Sometimes just a little dampening is just what people need. An older guy in my bike club loves this bike for big rides:
http://www.fujibikes.com/bike/details/roubaix-11 It's not an Ultegra, but you can always upgrade the components.
If you will be putting some short clip-ons and racing regularly, look for a bike with a bit more aggressive drop between seat and the handlebars rather than having them at the same height. Clip-ons on a road bike are not ideal in terms of dialing in the right hip angle and aero profile, but they can certainly help. There will still be a speed benefit if you plonk them on a totally plush setup but the geometry would be so different from your TT bike you might regret the purchase.