Hello Stephen,
Using the 'Advanced' or 'Expert' interface, in the 'Stitcher' tab you can
choose your output to be 'Remapped Images', which will save the aligned
individual images, but I believe they will be in TIFF format. It may be
possible to save them as JPEG but can't put my finger on how to do that at
the moment. It should be a simple process to to a bulk conversion using
other utilities if necessary.
Hugin's Preferences allows you to set whether the remapped images will be
cropped by default, or not.
Hope this is what what you were asking.
Cheers,
--
Regards,
Terry Duell