To allow the dichros to be moved on the baseplate, all you need to do is enlarge the hole that the mounting screw passes through. I suggest carving a narrow slot, in fact, so that you can move the dichro back and fourth. (This is the way my dichros are mounted.) Use a large, flat washer on top so the screw will hold the mount firmly in place on the baseplate.
You've got plenty of elevation adjustment on your lasers, judging by the picture you posted, so you shouldn't have any trouble there.
From the picture, it appears you'll want to raise the green laser some, and drop the blue laser a bit. As for the problem of getting the red and green beams to overlap perfectly while still getting them on the scanner block, that's where having some lateral motion on the dichro mount (from the slot I mentioned above) will help you out a lot.
Adam