With a little help from my friends (thanks Tim and Brian), I got my Yukon problems sorted out. The fundamental issue was that I had forgotten to install the Yukon test certificate before installing Yukon itself. Apparently, one of the pieces is signed with this, and the signature check fails during installation if the certificate hasn't been installed. So after re-running the install, everything appears to be working well.
The biggest mystery, though, is that all my .NET 1.1 stuff started working before I got Yukon running again. And I'm not sure what I did, although I suspect removing .NET 1.1 paths from the LIB environment variable might have been the key. Unfortunately, I wasn't very scientific in my desperate flailing. I'm just happy it works.