1- good idea

2- depends on your local code. We run a single 20amp 12-2 and share it between the DW and GD. A double circuit 20amp 12-3 is a nice alternative.

3- I too live in a pier and beam house. I use those wires stapled to the joists to help hold the insulation in place. When running parallel with the joists the wires are mid joist and not on the bottom. We foster Jack Russells and have had no problems in 15 years. We send a home run to a junction box in the center of each room, then come off the junction box to each outlet separately. This eliminates 'daisy chaining' and allows for easy future changes. Lighting is all done from the attic on their own circuit. Outlets from below with a dedicated line for each room.