Hi,
just one quick suggestion: Right now setup (i.e. putting binary bits on the computer) and configuration (i.e. setting up the database, IIS web site etc) are all part of the setup package. I think most server products from MS moved away from that model to a two step process: have the setup ONLY lay down the bits on disc, and then have a seperate configuration utility that does SQL database creation, IIS Website creation and whatever else is needed (i.e. see the new TFS 2010 setup experience, where they discuss this). In my own experience this also makes for much, much easier maintenance down the road, in particular updates will be much easier. MSI is fine for deploying updates to the bits, but when you have your configuration steps in the MSI as well, you are up for major, major difficulties that are really not needed.
Cheers,
David