Why will Project64 not recognise all the buttons on my pad?
If the control is not a DirectX button, a slider, an axis, or another recognised control (depending on the version of the plugin), it will not be seen by the plugin, simple as that. What you may be able to do it use your keypress emulation software that is provided by you gamepad manufacturer to emulate keyboard key presses. You then bind these keyboard keys in the plugin instead.