@dudleydes I realized that I had disabled controller 2 and 3 and when enabling them mouse is now also enabled by default.
By default mine was set to;
CONTROLLER_MOUSE_1=mouse
CONTROLLER_MOUSE_2=joy2
The one on Amiberry github is set to;
CONTROLLER_MOUSE_1=joy1
CONTROLLER_MOUSE_2=joy2
I had to set Mouse to my joypad (wireless ps4 joypad) to my mouseport, and also declare to Amiberry that its a mouse.