Bicycle Tutor

I am rebuilding a Fuji Professional 2004 frameset. What brake calipers would fit its 26 mm thick rear carbon stay and its 45 mm thick front carbon fork? Prefer ultegra or similar grade.
Thank you.

Two things to decide.
1) Make?
If Ultegra then you've already chosen Shimano.
2) Drop?
Measure from the mounting hole to the wheel rim and this will set the brake size (probably in the region of 49mm). and that's it.
http://www.bikepedia.com/Quickbike/BikeSpecs.aspx?Year=2004&Brand=Fuji&Model=Professional&Type=bike

Thanks, but maybe I did not ask the right question.
What model ultegra rear brake should I get so that it has a long enough thread to pass the rear carbon brake mount, which is 26 mm thick?
I have a spare Ultregra rear brake, but the thread is too short.

Oh! Sorry, I understand your query now.
You can get a longer "nut" to reach the mounting screw.
Such as:-
http://www.ribblecycles.co.uk/productdetail.asp?productcatalogue=WHEEBRZZ200
Ask your LBS or your online cycle suppliers.