You'll save yourself alot of cramps if you just get the far superior GameCube pad. Remember that the N64 contoller has only one analog thumbstick and if you map the second one on the standart yellow buttons, you'll end up being either short of buttons or short of triggers as there are no Y/X buttons on it.
Not only that, the GameCube pad is also superior when it comes to sheer comfort of using it. I will never understand what were they thinking when while designing the N64 pad they put three triggers on three different parts of the pad, as if humans had three hands. Sure enough it looks awesome, but it's not really pleasant to use as you will always be a bit too far from one of the triggers.