2) What microcontroller should I use in order to give me access to using tools such as QMK?
TMK and QMK support Cortex-M and Atmel 8-bit AVR MCUs. In short, your best friend will be Atmel ATMega32u4.
3) How/Where do I put mounting holes so that it will working in a standard 60% case?
Use positions provided by Pwner, as for the actual mounting hole, I use 7 mm plated pads with 2 mm hole diameter and 5 mm hole length for round mounting holes and 12 * 7 oval plated pads with 2 mm diameter and 10 mm hole length for side mounting holes.