@mcdermd
Hey guys, thanks for the wonderful software, which makes a lot of fun in the current situation. I bought one of those n64 controllers recently and have the same problem which is described above. So if I open the emulation the system pass back: SWITCH CO.,LTD. Controller (Dinput) not configured. I have no clue where I stuck.
Do you have any idea as you got it working a couple of days ago?

System:
RP4
RCB 701

What I did:
#1 I added "n64.configfile=dummy" to the end of recalbox.conf
#2 I added the correct controller configuratin to the mupen64plus.cfg

[SWITCH CO.,LTD. Controller (Dinput)]
version = 2
device = 0
mode = 0
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = "4096,4096"
AnalogPeak = "32768,32768"
DPad R = "hat(0 Right)"
DPad L = "hat(0 Left)"
DPad D = "hat(0 Down)"
DPad U = "hat(0 Up)"
Start = "button(12)"
Z Trig = "button(6)"
B Button = "button(2)"
A Button = "button(1)"
C Button R = "button(8)"
C Button L = "button(3)"
C Button D = "button(0)"
C Button U = "button(9)"
R Trig = "button(5)"
L Trig = "button(4)"
Mempak switch = ""
Rumblepak switch = ""
X Axis = "axis(0-,0+)"
Y Axis = "axis(1-,1+)"

Thanks,
wastl11