Agree that Ultegra would leave you hanging/wishing for lower gear ratios. One is better off using mostly a MTB drivetrain. I did a similar custom build on my Rodriguez UTB earlier this year. For the drivetrain this is what I did:

Shifters: Shimano Dura Ace 9 Sp. bar-end shifters. If I'm not mistaken, Shimano 9 Sp. Tiagra or Ultegra STI shifters should work as well.
Crankset: Shimano Deore M590 48-36-26t (replaced the 26t by a 22t) - It comes w/ integrated bottom bracket. This crankset came highly recommended here in the BF. It is very inexpensive crankset for a custom build, but it works really well for touring. The 48t works great for unloaded or lightly loaded rides such as faster Sunday rides or randonneuring.
Derailleurs: Shimano XT front/rear - Both work like butter!
Cassette: Sram PG-990 11-34
Chain: Sram PC-991

You need to decide whether you want to go with a 9 sp. drivetrain or with the new 10 sp.