Unfortunately, the mouse buttons do not yet work with ROM 920393. What a pity.
Do please try the bitstream that Gurce suggested above. The left button of any Amiga-compatible mouse should now work, if you have Amiga mouse emulation enabled in configure. The right button, however, will not work without making a special joystick extension lead -- exactly the same as would be required to use the right-button of an Amiga mouse on a real C64. The problem is that the Amiga mouse does not have a pull-up on the right mouse button, and nor does the C64 or MEGA65 on the pin used, because it is a POT input on the C64/MEGA65, but is a digital input with pullup on the Amiga, so far as I understand. Same goes for middle button of a 3-button Amiga mouse. I'm going to make up a test cable and confirm function with a MouSTer set to Amiga mode here as soon as I have time.