Hi.

If need for stitching scanned images is rarely, I'll suggest using Gimp.
With most scanners you can choose to not auto adjust the scanned image, and then the colors don't need corrections before stitching.

Newer versions of Gimp allows the user to put out guides, wich makes it easy to rotate the images (layers) to each other to fit.
I've already done it myself several times with scanned images.

I've also have bought a license of Autopano, but I use that program for photos only.