One thing to note with Autostitch: since it is a "demo" version of AutoPano Pro, it is somewhat limited in features, and the default settings are very lame. Before you do any photo stitching, first click on the Edit>Options menu and change the following options or you will get very low quality results:
Scale %: 100%
System Memory (GB): 1 (or more, if your computer has 2GB RAM or more)
JPEG Quality: 100
After you save the settings, click File>Open and then browse to the images that you want to stitch. One major difference between Autostitch and AutoPano is that with Autostitch you need to manually select the images that you want to stitch together and can only do one panorama/stitch at a time. If you do happen to select an image that won't link up with any others in the group it will usually just drop that image, but it can sometimes get confused if you give it somewhat similar images that don't belong. With AutoPano Pro, you can select an entire directory (or your entire hard drive) and it will automatically sort through all of the pictures and use a series of algorithms to separate them into individual stitching groups. If you really do have 10,000 images to stitch, it might be worth the extra cost, but that's up to you.
Also, you will need to use a separate image editor like GIMP or Photoshop to crop off the "extra" border area from the images produced by Autostitch while you can do it directly within AutoPano pro.
Please don't think that I'm trying to talk you into spending money on AutoPano pro if you really don't want to (I don't have any affiliation with them, but I really like the program), but it sounds like you might be in a position where it would be a worthwhile purchase. I would definitely try out Autostitch first and see how it works for you, since only you can decide if you are willing to work within the limitations of the free program for your project or if spending 99 Euro (about $150 US) is worth making the job a lot easier and faster with that many images.
edit: I forgot to mention something important that will make your life a lot easier with this project. While you are scanning the images, try to overlap the edges of each successive scan a little bit (at least 10%, but 25% is better) so that the program has enough matching data to work with that it can use to stitch the images together.