In reply to The Lemming:
> Yep I could not get Hugin to work with a handful of images. I'm guessing that it would crash my computer with 153gb of photos I created today.
Yeh, for a big job like this I'd just script it using panotools command line rather than use hugin. You should be able to do the alignment with just pairs of images in memory so no system stress.
Wintertree's suggestion of ffmpeg is worth looking at - I've not use its image stabilisation, but do use it to render the final video. Fantastically powerful once you get to grips with it!