Just make sure they don't cut the steerer tube until you have the bars where you want them (and I suggest not even then... let them use spacers to take up any slack until you've decided on your ideal handlebar height).

The other suggestion is build the LHT with a Sugino XD crank. I have the 26-36-46t, and I think you'll find that you will pretty much live on the 36/middle ring for most of your commute. I rarely/never have occasion to shift off the middle ring. My lbs couldn't get the Sugino, so I mail ordered it from lickbike.com for them to install (or you might consider Rivendell bikes... a little more expensive but I find Rivbikes/Grant Peterson a worthy cause

Oh... and don't forget to have them treat the inside of the frame with a rust inhibitor. I can't remember what it was called.

The shop that built my LHT was pretty hard-core spandex/weight-weenie crowd-caterers and lacked any sensibility towards touring... so both of these requests (high handlebar and the 26/36/46 chainring) were anathema.