It can be a bit confusing, but if you stare at it long enough it will start to make sense.
Find out which ones you have used, and mark them off the list. You'll also need to check the DB25 connector, and see if you have any extra pins.
I have the problem of having a few available pins on the MS2, (via the mods listed in the table), but I am out of pins on the DB25 (or very close to it). I plan to pop a DB9 on the case to break out those last few.
I see you have a stepper IAC soldered in (based on a quick look at your pics), which kinda sucks because it takes up 4 of those DB25 pins.
So, back to the table, any pin that says "programmable output" can be used as a fan control (but you may need to add a transistor to power the relay!)
Any that say "tacho" output can be used for tach control.
