Did you note to your wheel builder that they were for a Santana tandem and have 160mm spacing, not the standard 145?
I believe the new Ultegra brifters referred to only come in 10 speed, so .... more money to change some amount of cassette, chainrings, and chain, depending upon what you're currently running.
The other options on the brakes are put the front and rear canti-levers back on that it came with, or, see if a long reach Shimano caliper will reach for the front, (our final solution after mucho time/$).
If a caliper will work, DO NOT buy a high end caliper. Those are racing brakes designed to be as light as possible while still stopping a SINGLE bike. We got a tip about this from a fully-loaded tandem touring cyclist who had the same issues as we had. He recommended the "below the grouppos", unnamed Shimano calipers like
these since they were heavier and stronger. We also like the price!
Whatever rim brake you choose,
WITHOUT FAIL, upgrade the pads.
MAJOR difference. I like the KoolStop Salmons, others like the SwissStop ... greens, I think, but someone will correct me if I'm wrong.
We did the front caliper and the Koolstops, and I can bring down the front end of the bike so hard it puts my stoker onto my back even if I announce it. And lets just say that we're currently over a 400 pound team and leave it at that!
The other thing I'd want to say is that there is no such thing as "buying a tandem bike". What you bought is "your FIRST tandem bike". As you ride you will define what your uses for a tandem will be, and if the Santana doesn't fill the bill, then keep away from hi-dollar upgrades that can't easily be swapped to your SECOND tandem bike!
Hope some of that helps.