You might be interested in two options:
1: Geosynth: offline Photosynth for sale to 200+ employee companies (still completely automatic, though, as far as I know - i.e. no manual intervention like you specify), available here:
The pricing for this is somewhat outrageous, I am sad to say.
2: Bundler: the structure from motion algorithms from the research project "Photo Tourism" which inspired Photosynth, available here:
This is not a very end-user friendly bit of code, though, so unless you're comfortable with using command line tools, it's probably not for you.