I finally got around to spending an afternoon on this, and I think the basic concept of "evidence inevitably goes to universities, universities inevitably provide local specialized resistance, universities semi-preventably share information with each other" is cool and rad. Also does a very good job communicating a more industrial revolution style flavour, which I assume is what you're going for with stuff like the new portrait art and the depth charges. I also dig the specialized cult and custom plague approaches.
I've only played one game so far, but the profile and menace hits for evidence and the sheer number of messengers that bounce around the universities were kind of a feel bad, and I worry that linking world panic to evidence uncovered might have a perverse effect toward making players do fewer interesting things and more just feeding more resources into the things they've already done.
So I'd say it's an excellent high concept, I can't offer sophisticated advice on the exact form the evidence economy should take (plus some powers like Well of Shadows still don't seem to reflect their description), but I would encourage you to tinker with the evidence economy as you work.