Steve,
With regards to your footing and foundation, it depends on your time vs. money equation.
If you have more time than money, then I would say slip trench a concrete footing and build your stone wall from scratch.
Or you could spend more money and put up a block wall and face it with stone.
Or spend more money and pour a concrete frost wall and build your stone wall on top.
I'm not a big fan or using stones as filler in concrete footings or walls. Concrete doesn't bond with stones like mortar does, and stone weaken it structurally.
Concrete with lots of stones...bad.
Stones with a lot of mortar...bad.
Concrete with small stones (aggregate)...good.
Stones with joints of mortar...good.
Using large stones as a footing below frost line is how many barns were built. But that is a lot of work and is difficult to build off of especially if the stones don't have a relatively flat surface to begin your wall.
Back-filling the foundation with 2-3in stone will help with the water and frost issues, by allowing any rain or moisture to drain straight down instead of being trapped up against your stone wall causing damage when it freezes. Also, gutters at the eaves with drain spouts will help the water vs. stone foundation conflict.
Rooster