1. I think you would have to make it redundant unless you want to go into the games played on the classics panel and configure them to use joystick 3 U/D/L/R
2. The answer is yes, but I would connect all the buttons to the minipac - see #4 below.
3. I would think you would need 3 different Shift buttons - if not you would be shifting the mode of all three GP-Wiz 49s at once.
4. I would connect all the buttons to the Minipac (unless that causes a problem in other emulators). My experience has been that sometimes MAME dumps the start/coin button configuration from the GP-Wiz 49 if is ever not connected when MAME is launched.
5. Minipac due to the reasons listed above. My experience is that it's easier to configure in MAME that way.
Don't get me wrong, I love the GP-Wiz 49, but since MAME is setup for keyboard defaults, I've found it's easier to configure (and keep that configuration) using a keyboard encoder for button inputs. I simply don't know for other emulators as MAME and Daphne are all I have used.