You're right, flash panorama can be a solution when you have to be handeled and limited in iso settings.
Autopano try to be easy and that's cool if you have fun with it
Fuji have good colors, enjoy
For this particular panorama, you can try from the "center" of the scene, keeping large overlap betweek image (decreasing light inconsistencies due to flash), and with even more rows than you used before.
If you manage to keep the camera in the same optical center when shooting (otherwise you'll have parralax errors) you'll have great results !
ptss: buy.autopano.net will be opened soon.