Just to add my two cents: I installed MS Project 2002 server on the box I
use for SPS and when I did that several aspects of SharePoint became
disabled. Once I got MS Project 2002 back off the server, it took some time
to repair the damage (which means in this case reestablishing settings via
IIS mostly having to do with permissions).
For example, the category Web part died for a time until I could get the
settings back to normal. Also, documents that had been checked out, edited,
and republished could not, after the install/deinstall of Project 2002, be
found via the search function (so I'm guessing they were not indexed). It
took some time to return all of this to normal.
It makes sense to install Project 2002 on a clean box, after installing SQL
Server and the OS. If you need to search the Project store as a resource for
SPS, can't that been done? Whatever Web pages Project produces should be
available to SharePoint like any other HTML resource.