1) Change tracking. Technical hurdles (and they're huge) aside, it would be great not to have these links break when text is added/removed.
2) Better onsite instructions. I knew how it was supposed to work, and it took me a bit to figure out that clicking a sentence highlighted it. Perhaps a tooltip?
I think the deeplink suggestion is good. If I stumbled across these urls, I might just think it was some evil tracking code or something and strip it off, deeplink is meaningful and gives me a clue that it does something clever. Great work btw.