Well... call it coincidence, providence, or something. I submitted a ticket to 3Essentials hoping to possibly see if it might have been a problem on their server (having four sites hosted on the same server, two with problems, I didn't think it *was* a problem, but running out of options). They answered back that they did have a problem and were resolving it and that the error *could* possibly be related, but since my other two sites were not having the same problem I wasn't thinking so.
Ultimately the problem seems to be coming from when the site was recompiling on ApplicationStart, so I knew it probably had to do with something that wasn't precompiled. The only two modules that were in common between the two sites in question that were not precompiled modules were the Text/HTML and the Survey 4.0.1 (or is it 4.1.0? dunno...). The other two sites on that server also had Survey installed, but they had 4.5. I doubt that was the cause of the problem, and this is where I am saying it is likely coincidence, but I haven't seen the problem since then (and it was frequent enough before that, that it should have occurred again by now).
Long story short, I'm pretty sure it had nothing to do with the Survey module and was more likely really a server issue that they happened to resolve at/around the time I uninstalled the Survey module. Either way, I'm just happy those sites are working again full-time. Always sucks when a site is having issues.
(I'm also more inclined to believe it was the server because both those sites have had the survey module installed on there for months without problems).