tenors,
i just realized you're getting a deore hollowtech II crankset. This is very nice; much nicer than the alivio you'd originally planned. did you get the "trekking" version, with the 48t big ring?
I wouldn't worry too much about the geometry that the slightly different axle-to-crown dimension is going to get you. This is a commuter/hack type of bike, so you're right not to obsess over it.
IME, bikepedia is a wonderfully useful resource. However, we cannot expect it to be 100% accurate in terms of being thorough, or even always correct. Some colors may be missing, or attributed to the wrong model year. We also need to remember that manufacturers often switch spec in the middle of the year. This is esp true when transitioning between threaded and threadless headsets, as the frame can be identical. Basically, if you start 1996 with a 1" threaded bike, and you know you're switching to threadless soon, you're going to keep building the threaded version for as long as you have threaded forks, and not a moment longer.
-rob
PS- tenors, finish this pig pronto; i'd love to see pictures of the complete!