I have had Hugin installed for a while now to stitch panoramas. But haven't been able to get the autopano-sift plugin to work correctly. I left it for a while, but coming back to it I thought I'd ask if anyone has any experience with it, or suggestions.
Can't help you with Hugin, but if you have access to a Windows box (or just a VM), try Autostitch. http://people.cs.ubc.ca/~mbrown/autostitch/autostitch.html