[totallymike]

I'm hardly a pro at using bootstrap, but we have been dealing with a few of these things, and I can tell you how we've handled some of these questions:

* How do I add icons without peppering span.glyphicon.glyphicon-X's all over my markup?

This one's fairly simple--you still need to add a class to the span, but you can extend the glyphicon.glyphicon-X bit into a particular icon and call it a day:

    .foo-icon {
      &:extend(.glyphicon);
      &:extend(.glyphicon-foo);
    }

* How should I organize/maintain all of my LESS files as my stylesheets scale?

I'm not sure there is a "right" way, but I'd suggest keeping like things together. You're going to end up with a number of rules that are either dependent upon each other, or at least similar in goal, and they can live near each other. In theory, future refactorings will be easier that way.

* Are there any optimizations I can consider when I'm only using a bit of Bootstrap's functionality?

http://getbootstrap.com/customize/

^ Do that :)

Good luck. If you find answers to the rest of those questions, pass them to me!!