sargentkm, I agree, it's confusing when a glitch coincides with changes that our algorithms make with regards to a site and I wish we could have avoided that (well, I wish we could have avoided the glitch altogether, but that's life :-)). I can however assure you that the two are definitely not related; if you are still seeing changes now that the glitch has been resolved, then those changes will be due to something else. Google's algorithms are constantly being worked on, so even if you have not changed anything on your side, it might be that our algorithms' view of parts of your site changes over time. So personally, I would really not fuss too much over the technical issues we had, and instead focus on what you can do on your side to improve the bigger picture of your site.
I realize that working with user generated content makes things a bit more complicated, or at least it requires creative thinking... I imagine you probably have much more experience and many more ideas around that than I would, so I'm certain you'll find something in that direction :)