There's one 44-pin chip in the gamepad.
My PC-FX gamepad:
NEC Japan
65612 107
9440EX007
My FXGA gamepad:
NEC Japan
65612 107
9515EX011
A very quickie pinout, it may have mistakes, I just made it. :b
The question-mark pins are COMPLETE GUESSES. Hopefully, the protocol is simple, just sending 32-bits of data each strobe/reset/request/whatever, but I don't know.
(Looking at the joystick port front-on on a PC-FX)
A B C D
E F G
A = Reset?/Strobe?
B = Input/Output select?
C = Data?
D = +5VDC
E = GND
F = Clock?
G = GND
Inside the FX gamepad, from left to right, top of the circuit board, the soldered pins:
(GND), F, (GND), A, B, C, D(+5VDC)