Hey guys, just a follow-up.
My brother and I cleaned the stem very vigorously with hot water, lemon juice, and baking soda. There is still a distinctive smell in the large ball piece on the bottom, so we weren't sure how well it would do. The longer piece of the stem has a slightly less noticeable smell to it. We packed a bowl, hopes a little low, and we're currently enjoying one of the best hookahs we've ever had.
Amazing fix, thanks everyone.