Dave,
I'm not sure where you're at with this project, but I honestly think your best bet is just using tons of layers Photoshop. A number of years ago I made a trail map as a volunteer project and it was by far the quickest and easiest solution. After all the end map is going on to an 8 1/2" x 11" sheet of paper so you don't need complete pinpoint accuracy.
Wouldn't you lose a bit of the accuracy by doing that?
You can't just take 2 gps files and merge them?