1. I have the Schluter kit here - What is the best way to mark the target height of the top surface of the kerdi drain for the plumber ?
It sounds like you have removed the existing shower pan plus the entire concrete slab under the pan. Is this correct?
Remove the center section of the Kerdi tray and use it as a guide for the plumbing rough-in height. You first need to determine your final slab height then using the Kerdi tray pc and Kerdi drain you can calculate the stand pipe height.
What is the best concrete to use for the subfloor ?
Use regular pre bagged concrete mix.
Concrete should be a minimum 3" thick for non load bearing slabs.