Step 10: Accessory: SNES Adapter
First take one SNES controller extension cord and remove the end that would plug into the console (male end), but keep about 6" of wire near the end incase you ever need it again. Next, cut the NES controller extension port cord about 6" from the part you would plug another controller in (female end).
Now you will splice the cables together, except the yellow and red wires will be crossed. So the red NES connects to the yellow SNES and vice versa. Once you spiced the cables together and used some electrical tape (or that nice heat shrinking wrap for splicing) you now have a cord that has a female SNES port and a male NES port, and it will act as your adapter for using an unmodified SNES controller on your nes ports. As a bonus, this cable also works in the original NES system if you like the SNES controller better.
NOTE: One side note, on some of the cheeper generic extension cords they use different colored wires. So if this is the case all you have to do is get out your multimeter, find a nes and snes controller port diagram and trace your wires connecting all the wire functions to the same function on the other controller port. You won't cross over any color wires, you simply hook up your power to power, clock to clock, etc... It is more of a time suck than hard to do. Just know how to trace your wires in the cord from your multimeter manual and compare snes and nes controller port diagrams.
With this your hardware modifications are complete, now onto software.