I currently have Shimano BR-600 brakes on a Surly Pacer.
I will be doing a rebuild on a Trek Pilot using the Ultegra 6600 groupset.
I will need standard reach brakes for the Pilot.
It would be nice if I could just swap the Br-600 brakes over to the Pilot and use the 6600 brakes for the Surly.
The Br-600 brake pads are adjusted way up near the top of the brake arms on the Surly. I've taken some measurements. It looks like it would be close as to whether or not the 6600 brakes would work or not.
I think that Surly designed the Pacer with 50mm reach for the brakes. This means that, practically-speaking, you can use lots of normal "short" reach brakes (technically rated 39-49mm reach) just fine on the Pacer. However, it's not guaranteed to work and Surly recommends "standard" reach brakes (47-57mm).
I'm guessing that it'll work for you. If it doesn't, then you should just buy Nashbar's house-brand standard-reach brakes and use the 6600 pads on there.