A few options you can try:
1) I use VirtualDub all the time to edit my Suzi Perry vids for the website. You can "Crop" the video like shown on
http://nickyguides.digital-digest.com/vdub-filters.htm (see Britney Spears Video image)
2) How many Frames is the GIF going to be? You could use Full AVI & Screen Cap the Frames & cut the section you want in PaintShop Pro....