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what vr set do you use?
did you tried to map the controller with your vr application? (however you need to use only the trigger in menu, then use gamepad and keyboard in game)

SteamVR.
Index + Index knuckles/Keyboard

mmm i don't honestly know how to help you, i don't know how your controller works,
i'm making the game testing with my HTC vive but i had feedbacks of people managing to use it also for other sets.
WAIT are you playing the version 0.2.55 or 0.3/0.3.4? in 0.3+ you don't need vr controllers anymore