We have heard about two issues from customers that are upgrading from TFS2005 to TFS2008 that also wish to upgrade Conchango’s Scrum product (SFTS) from v1 to v2:
1) Uninstalling Conchango v1 before the TFS 2008 upgrade causes the WSS3.0 prescan tool (run during the TFS2008 upgrade) to fail since the Conchango uninstall removes the WSS site template.
2) Uninstalling Conchango v1 AFTER the TFS 2008 upgrade (and WSS 3.0 upgrade) in order to install Congchango v2 is successful, but existing v1 Sharepoint templates will receive a 404 error as the site template files are missing.
Conchango is aware of both of these issues and has a fix in the next version of their software, they have also posted a fix on their blog site which people can install now if they are experiencing the problem. The post can be found here: http://blogs.conchango.com/sfts/archive/2008/04/28/sharepoint-fix-for-scrum-for-team-system-2-1-upgrades.aspx.