Go with an Ultegra double (109.5) bottom bracket if you get the Octalink. Otherwise, an ISIS BB will be fine.

As for the braze-on derailleur, it's possible it won't adjust low enough. Mine didn't on my '03 5500. You have two choices - your Trek dealer can order a customized tab that will allow the der to go lower or you can file it out yourself. I filed mine with a rat tail file and it works great. PM me if you need info or pictures.

55/Rad