Are you going to take the books and magazines apart?
I have a Brother MFC-6490CW that I bought because it is huge (does A3) and a feed scanner for a sweet price. I think it's out of production now, but it is rad. I bought it to be able to drop a stack on animation into, and it's great for that, and just scanning large artwork in general.
I don't know about pdf software, but I'll bet you could get most of it done with PS and some simple actions.
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