I think 8 buttons per player will be plenty. If you don't count the control pad (probably 99% of the time it has the same function as the analog stick or is not used at all), there are only 9 buttons, and I'll bet 99% of games either didn't use the L button or it had the same function as the Z button.
As for configuring it, I would think it's very game dependent. Unfortunately, Project 64 does not allow different controller assignments for different games (unless it's been updated, I haven't checked in awhile). A couple of workarounds though: You could try to find a key assignment set that works ok for most of the games which do not allow you to customize controls, and then customize the controls and save in the games that do. Alternatively, you could customize controls using autohotkey scripts.
EDIT: Fixed a typo that made it really unclear what I was saying about the L and Z buttons.