Yeah, that all occurred to me, yet I still turned off squid transparent proxy, even though I knew it shouldn't affect HTTPS traffic, and to be honest, I actually didn't expect moving my ethernet connection from the pfSense box to the original router to make a difference, yet it did.
Anyway mystery (mostly) solved after stepping back and looking at the packet captures more closely. The PDF file is hosted on an Amazon CloudFront content delivery network. It turns out that I was downloading the PDF from different servers depending on which device I was using as a router. Not too surprising in retrospect, since different DNS resolvers could have different answers in their cache. I think what really threw me (apart from sitting at my computer for too many hours straight), was that curl always downloaded the correct content even when I was connected through my new pfSense installation. For whatever reason, curl on OS X was getting the 'good' IP consistently, while the browsers consistently used the 'bad' IP that matched what I would get when using dig against the pfSense resolver.
In any case, my confidence is restored in my new installation, and I guess I'm just going to have to live with curl vs. browser DNS resolution mystery.