Flagstone on Wood Floors
First lay a minimum of 1" of plywood over the joist in 2 layers. The first layer should be nailed and glued to the joist. The second layer should be nailed and glued to the first layer. Make sure the second layer is laid in the opposite direction and nailed into the joist below. Certain flagstones are made in a uniform thickness and can be set in an epoxy type of cement. Grouting between the stones should be a mixture of 2 parts sand and 1 part Portland cement. Mix to a workable consistency with 1/2 water and 1/2 Flexcon.
Most other types of stone where the thickness is nominal, lay plywood as above.
Then lay down building paper and nail metal lath. Overlap the joints 2" and nail tight into the joist. Lay down a thin later of 2 parts sand and 1 part Portland cement and mix with Flexcon to workable consistency. Spread this over the metal lath, just enough to cover the metal lath. Let this set up, but leave it with a textured surface suck as a scratch coat (cut a piece of metal lath and drag it over the surface to make it textured). Next, set the stones with the same mixture of cement as above in method #2, keeping the setting bed as thin as possible. After the stones are set and the cement is hard (next day), grout between the stones with the same cement mixture as in method #1. Be sure to keep the stones clean as you work. Sponge off any cement that gets on the surface immediately.