IIS Manager is loading the wrong internal DLL

I'm on Windows Server 2012 R2 and IIS 8.5.9600 that was working fine in a development environment. All of a sudden IIS Manager is giving me errors about missing functions when trying to use the UI, for example Microsoft.Web.Administration.get_StartMode() when trying to view the application pools. And sure enough, when using ProcessExplorer I can see that IIS Manager has loaded the 7.0.0.0 version of the Microsoft.Web.Administation dll that does not contain these functions. Also in the GAC is the 7.9.0.0 version that has the missing functions.

I've tried reinstalling all of IIS by removing and re-adding the feature, but the problem persists. I've tried to remove the 7.0.0.0 version from the GAC but it wont let me since "it's required by another program", even after uninstalling the web server feature and I can find no other process that's using it.

How can I clear out this mess without a complete server reinstallation?