Beautiful diagram!
This link should help with the recharge port:
JediMasterTim's Wiring DiagramBasically, the recharge port just goes between the battery and the board, and the port acts as a switch to open the circuit when the kill key or charger cable is inserted.
Resistors are calculated using the formula (from the manual): R = (Vsupply – Vled) / LedCurrent. So, (3.7 - 3.47) / 1 = 0.23 ohm resistor. That said, check out the "Drive Adjustment" section in the NB3 manual, page 21. You could technically use this technique and skip the resistor altogether.
As far as using a switch as a kill key, yes it's possible; however, said switch needs to be able to support the current coming from the battery. Regarding the red Graflex button, as they are received from TCSS/Korbanth they are set up to use a momentary switch, you would need a latching switch to act as a kill key. If I were to use this technique, I would put the latching switch on the negative leg between the recharge port and the board.