"For example, if you need some extra back tilt of the neck and remove a shim stamped "06" from the neck-to-body joint, then you would replace it with a shim stamped "04", slightly thinner than the original factory installed shim. That changes the neck angle in small repeatable increments."
Just to expand- from what I've read, the shims are replaced in pairs, so that if in the above, the 06 would be paired with, say a 42, going down to 04 would mean going up to 44 for the paired shim. So in other words one shim is replaced with a narrower one, the other shim with a thicker one.
And for what it's worth, on my GC8 I did a minor amount of shaving on one shim and, if memory serves, placed a few layers of aluminum foil to thicken the paired shim to change my neck angle ever so slightly. It did work to get my action down where I needed it.
I imagine your luthier could come up with his own mahogany shims if he needed to, using your existing ones as a model.