The parts I want for my custom saber are not available on the parts pages do I need to call to set up a special order?
Or email them. While US does sell parts that are not listed on the site, they do not sell all possible saber parts.
Or do I have to buy each empty saber and scrap the parts I don't use?
No.
Will the web site get updated at some point with their full inventory?
I doubt it. US has always sold more than they've listed, but some are only available by special request.
Have you tried the TCSS website? They've got tons of parts.