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mapstitch looks like a good place to start. I suspect it relies heavily on overlap between the maps it's trying to merge, in order to automatically determine the alignment between maps. If you'd like to use it, you should make sure that the map pieces you make have a significant amount of overlap.

The other alternative here is to simply use an image editor to merge your maps by hand. Map files are just pnm image files, which can be opened and edited in an image editor such as gimp or photoshop.