Firstly, in order to do what you want, I wouldn't scan the two halves of the image as PDF's. I'd make them jpegs or tiffs. And make sure you leave a small overlap of image on the joining edges, if you can. If you can't do that, then it might be better to create three overlapping files, rather than two.
That should enable the sections to be stitched together in any decent image editing program.
Or you might find it easier to use a specialist panorama creation program to do the stitching. For a free one click here