[SteveC]

That sounds like pretty standard phrasing to me also. Destination first, route to your destination, then any special instructions for the route (hold short being the most typical). I really can't think of a better way to present the information any clearer without clogging up the frequency unnecessarily. With that pattern you get the overall plan, the details of how you're going to complete the plan, and the important instruction given last so you'll more easily remember it.

Controllers know that new guys sometimes need a few trips to learn the ropes at their airport. Some of them might not have much patience with that, but that's not your problem, is it? Here is a hint you might use in the future: don't ask for clarification more than once. If you're not sure the first time given an instruction, ask for clarification as needed. If you're still not sure, just ask for progressive instructions. Here is how it might go in the situation you outline:

"Boston ground, Comair 1234, taxi."
"Comair 1234 runway 9, taxi kilo, mike, hold short alpha"
"Runway 9, taxi via kilo and mike, hold short...where (?) for Comair 1234?"
"Comair 1234, kilo, mike, hold short alpha!"

"Ground, Comair 1234 request progressive."

It doesn't tie up the frequency any more than needed, and helps keep both you and the controller from making a potentially nasty mistake. Nothing else needs to be said between you and the controller, you both are now on the same page, for sure! (I learned that trick from a 13,000 hour pilot. First lesson he taught me is to check your ego at the cockpit door because nobody knows everything. Never pretend you know something that you don't, and don't worry if someone else thinks that you should have known something that you didn't. If it was really something that you should have known - make sure you go back and learn it later, but never make a problem worse in the cockpit by bluffing.)