I'm pretty sure I've got this sorted out now. It's set up pretty close to how the N64 layout was. I changed the rumblepak switch to requiring a hotkey to be activated. Current setup is below.
DPad R = "button(13)"
DPad L = "button(14)"
DPad D = "button(16)"
DPad U = "button(15)"
Start = "button(9)"
Z Trig = "button(6)"
B Button = "button(1)"
A Button = "button(0)"
C Button R = "axis(2+)"
C Button L = "axis(2-)"
C Button D = "axis(3+)"
C Button U = "axis(3-)"
R Trig = "button(5)"
L Trig = "button(4)"
Mempak switch = "button(11)"
Rumblepak switch = "“J0B8/B12”"
Analog axis configuration mappings
X Axis = "axis(0-,0+)"
Y Axis = "axis(1-,1+)"
Joy Mapping Stop = "J0B8/B9"