I don't know if this helps anyone else, but here's what happened to me. In messing around with some other stuff in IIS trying to get everything integrated, I marked the /forums subdirectory in IIS as an application. DOH! Whenever I tried to hit a forum page it couldn't find YAF, and no wonder.
Removed the application on the subdirectory and presto!
The integration works great. Not a single problem.
Thanks for everything, and I hope this helps some other poor, miscreant soul.