From the sound of things you should be able to follow Mickey's lead on your construction method.
I would first remove the Topsoil (30-40 cm) to the perimeter (to be re-used later)
Then excavate about 1/2 the depth of your clay (30 cm) to build up the sides of the pond above ground. That will leave you a 30 cm clay bottom and clay sidewalls of sufficient depth.
Then you can re-use the topsoil to cover the top and exterior walls of the pond for re-seeding with grass, etc... for aesthetics. (No trees or shrubs close to the pond as they will send roots throgh the clay and cause leaks).
Whatever you do don't break though to the shale. Unless it is harboring a natural spring (unlikely) you would never be able to hold water with a shale bottom.
As far as the bentonite goes, if you need it a mixture of the Calcium Bentonite and Envirobent (probably Sodium Bentonite with lime) should work well for you. Re-liming a mudpond from year to year is common practice anyway and the high ph won't last long when the pond is re-filled.
BTW, what is the ph of your well water. Tested fresh from the tap and after resting for a few hrs. In most cases it should be low from the hose and higher after it rests.