@Penjack7 I can see you've been doing your homework, good!
Regarding the ESCs: I removed the +5V from both the signal/BEC wires. See image below. The servo rail on the Pixhawk does not need to be powered to work. however, if you wish to power it, you may leave one of the +5V wires on one ESC, but not both. Otherwise, they will overheat each other. I've seen at least one fire where more than one BEC +5V was connected. Another option is to clip both +5V BEC wires and plug in a dedicated 5V UBEC. This is what I'll probably end up doing if I find myself ever needing to power the servo rail for whatever reason.
I'm unsure I about the Futaba equipment. I used a Spektrum DX8 G1 plugged into the SPKT port. As a note, I'll be ditching this on the next upgrade and moving to a pure joystick setup.