Because both of these projects assume a web application being used locally, it might make sense to do a Prism or XUL Runner app, specialized to host them (cf. http://wiki.oxymoronical.com/Projects:MozDevDocs)

The local MXR would index only the trees in the kit (see the Source Code section). The look of the HTML pages should be modified somewhat to make it clear that this is a separate resource to what is on the web, and therefore the code indexed is not the same.

Where MDC is a wiki meant for distributed collaboration, the documentation in the kit is read-only. Furthermore, where wikis prefer writers to readers, the documentation in the kit needs more top-down organization to link everything together (cf. MSDN). Getting rid of the wiki would mean that the content can be distributed as files vs. needing a web/wiki server.