Chuck sounds like a beautiful project! The idea of using the plywood as a template is great if you don't have the muscle power to be constantly moving the stones back and forth.
Using mortar to affix the stone inplace is the only way to go. Use a stringline to find the highest point on the wall and that spot is where you want to start mortaring your stone on the wall. Don't put down a cap first, that is just another step and a waste of $. Be sure to butter your stone with a slurry of portland cement and the surface that you are adhering to, this will give you the bond that won't fail.
Good luck!
Matt

I really like the look of long pcs of stone for capping walls, but there are some potential problems with the 6' lengths in your situation. Your wall is going to move as the years go by, particularly with your cold winters in Mass. The long lengths are far more likely to pop loose, or possibly even crack, as the wall moves. If you cut them in half, they would be a heck of a lot easier to handle, and the inevitable separation from heaving would be less of an issue.

What you could do is put a spot of weak mortar under the ends of your caps and get the joins and the level right first and push the rest up under afterwards. I would not bother with the adhesive. If you know how to use lime or lime putty you could consider that. There is no doubt that your wall will settle so a weak mix will offer less resistance than a cement rich mix. The weight of the caps will hold them in place.