You can buy the expansion card PC-FXGA in three different versions (see also
here and scroll down to the bottom), the main difference is the slot format and software, and then you have the real PC-FX hardware in your PC-98. The card itself features the same joyports as the original PC-FX hardware. The computer's HD is used as a memory card plus the software bundeled with the GA enables you to write your own FX programs. These programs can only be run on a PC-FXGA enabled computer and not on the real hardware.
So the monitor and the computer's HD is used by the PC-FXGA. I don't know if the PC's mouse is supported, I guess you need the FX mouse.
I have two PC-FXGA cards but are lacking a compatible computer, so I haven't tried them myself.