I sent an email to mapfdbk@microsoft.com, but am going to post it here as well.
My company previously had an installation of MAP on one of our servers, and due to space issues, the system required reconfiguration. – We went through the process of completely uninstalling MAP and all of the SQL components. Followed by, a reboot.
From there, we reinstalled SQL Server 2008 R2 Std (64-bit SP3) on a different drive letter/path and rebooted again. – However, when we attempted to install MAP 9.9, it rolled-back citing that “Setup failed to update the product. Fix the issue and run setup again.”
OS: Server 2008 R2 Datacenter Edition SP1 x64