D-Input support is removed if the game detects it's running at a certain lower framerate in the first frame of the application since the original steam release so it will have issues with Switch Controllers even if you don't use the mod.
The game was not designed to support Nintendo Switch controller layout and it won't be supported due to how the game was designed. Maybe in the future the input system will be replaced with SDL but I cannot promise.
I presume you are mentioning Sunfire Forest but the pause bug has been already fixed since the first release of the mod. Maybe record footage of it next time and send it here so I can try replicating it and hopefully find a solution to fix.
You can also report bugs in my discord server which you can find in the description of the mod page.
Thanks for playing!