I tested both joystick ports and measured +5v between the two pins mentioned, so it would appear my fuses are ok.
Yet I still have no mouse, just buttons on port 1, don't know how to switch ports to try the mouse in port 2 if that's possible.
It looks like the resistor at EMI401 is burnt. I can't make out the color bands, but the first one is green. Available documentation suggests that this is a 1 Ohm resistor, though clearly mine is not. The burned/scorched parts hide the colors of the other bands and I can't find anywhere that lists the resistor value for EMI 401 on my A500 rev 5 motherboard. I suspect the value of the resistor is different on different revisions and I don't want to put the wrong value in there!
Anyone else have a rev 5 that could give me the color bands of EMI 401 ? (It's near the JOYSTICK 2 port)
I'm guessing based on a few pictures available (all hard to read, sadly) that it's GREEN-BROWN-SILVER-GOLD or something close to that, which suggests 0.51 Ohm.
According to the service manual, EMI401 is a noise filter listed as 100pf. On the actual schematic, its drawn as a resistor with an extra lead going to ground... I'm assuming that's a 100pf capacitor to ground. It says 4.7 next to it, but no multiplier... In any case, the 5v to both joystick ports goes through it, so if you've got the 5v on the ports, I'd say EMI401 is OK.