xbox 1 controller RB, LB, X, Y, A, Dpad, and menu buttons not working

The bottom motherboard is responsible for all of the buttons you mentioned. Replacing this part will most likely fix your buttons. It is odd that your controller has power, though. The micro-USB port is also on the bottom motherboard. If your controller works plugged in, then I suspect that the exact problem is a couple faulty pins in the connection between the bottom motherboard and the upper one. Visually inspect the pins on the square connector that connects the two boards to make sure that there is no visual damage or discoloration on the top board (since you're replacing the bottom one). If the top board looks intact, then I highly suggest replacing the bottom board.