The only things you've given a reason for upgrading are the brakes. If you're using non-aero levers, switching to aeros can make a night-and-day difference in braking. Adding Kool-Stop salmon pads will, too.

Beyond that, what are you hoping to accomplish? Assuming that "upgrade" means "improve," what's wrong that needs to be improved? Unless you absolutely demand the bewilderment of tire choice requiring scientific notation to number the choices, there's nothing really wrong with 27-inch wheels, especially for us larger guys. And that the rear hub uses a freewheel is not really an "issue." Freewheels are readily available at a good LBS or by mail, and if you'd like one more gear, a 7-speed freewheel can frequently just be spun on in place of the 6.