Last time I mentioned Aaron Stebner's sample programs for testing the registry for framework installations. Aaron has a few more tools dealing with framework installations that you may find useful.
First is the framework setup verification tool, which can perform a variety of verification checks against a framework installation. These checks include verification of files, directories, and essential registry keys and values used by the framework and execution tests of a few simple framework applications. If you're having trouble determining whether your framework installation is correct, this tool may help provide some additional information.
.NET Framework Setup Verification Tool
Second is the framework cleanup tool, which can scrub away bits left by different versions of the framework. The cleanup tool deletes files, directories, registry keys and values, and installer data that may be left behind by a framework installation. This is intended for use when a framework installation is broken and normal installing and uninstalling no longer works.
.NET Framework Cleanup Tool