Legs and Z axis are really dependent on your use. For CNC Routing you want it as short as possible, the height of your material plus the length of the bit is a great starting point. The shorter you go the less you’ll have to worry about rigidity, which allows for deeper cuts or higher speed. For 3D Printing you have to base the height on the height of the biggest model you need to print. Higher than needed and you’ll see artifacts on the layers when the Z axis wobbles. If you don’t need a printer with that large of a bed area it’s better to use the MPCNC for routing and build a MP3DP for printing.
End stop wiring is going to depend on which end stops you use. The simplest ones are just a contact closure and they connect to the S and - pins on the RAMPS. Powered end stops, such as optical, also require power and that’s supplied by connecting to the + pin as well. End stops aren’t really needed for routing since you zero after manually placing the bit but are fairly important for 3D printing, if only because the 3D printing software expects them to be there.
The Emergency Stop wiring is going to need to be wired as the manufacturer of the ES switch requires. It’s typically used to cut the AC power to everything, so the router and Arduino/RAMPS both shut down at once. If they don’t provide wiring instructions I’d wire a single pole switch to shut off the hot side of AC (usually the black wire) and a double pole switch to cut both hot and common (usually the white wire). I have my electrics all connected through a power strip, and my E-Stop is wired to kill the power to the strip. It’s not ideal because I’m using a laptop to control the Arduino, and the laptop keeps on running after the switch is thrown, which also keeps the Arduino up since it’s getting power from the USB port, but the steppers all shut down when the 12V supply goes away so it’s still workable.