Or a semi automatic mode, where the user has to scroll between each screenshot and your programm connects all those screenshots automatically?
we must be thinking alike, that idea just occured to me as well..
there are 3 hard parts about scrolling window capture:
1) determining the overlap between pages
2) determining when to stop scrolling and finish the capture.
3) sending the scroll commands to the window (page down or line down).
often all 3 of these issues can be done automatically, and scrolling window capture works.
sometimes 1 of these issues proves too hard for sc and it fails.
but a semi-automated process where the user is responsible for doing the page down commands and knowing when to stop, could be the perfect compromise with hard cases.