Ohhh, I have experience with this! I usually do it manually in Photoshop. I don't really know how to give advice on it, though; I just put the images together in two layers and then move them and erase/blend them until they fit. It helps if you take three scans - the first half, the second half, and a middle that covers a little of both.
But, if you want, you can send me the scans and I'll put them together for you.
My new drawing is all finished but it is A3 and no matter what I do, I can't get it to stitch together well I'm not good at these things Normally I use MS ICE and it stitches for me, but it won't recognise the scans this time for some reason. Ariel, if your reading, I did it your way, but I can't fix it
So, blah blah, sorry .... I took a photo and those skills are just as crap as my scanning skills are
the solution is simple - you have to scan in more parts MS ICE used to drive me insane until i figured that it's because i need more parts of the drawing overlapping - meaning more scans. you can scan in 3-4 parts instead of just 2, it won't give you any problems anymore