Everyone has their own way of holding a 2600 joystick. I've always held it with my right thumb on top of the stick. On an original 2600 joystick, that meant my right hand was stretched out, and got sore pretty quick. So I shortened the joystick shaft a bit, and found that did the trick. It gives the 2600 a much more comfortable and responsive feel. Sort of like blending the best of a joystick with a gamepad. (Similar to gamepads with a short screw-in joystick handle.)
If you decide to start chopping up your joystick, I'd suggest taking off a little bit at a time. You can always make it shorter, but you can't make it longer (unless you get a joystick repair kit).
Here's a diagram of how I modded my joystick. Just take the stick apart, and cut where shown. (You don't have to remove the retaining ring or circuit board). The rubber cover will stay in place over the shortened shaft, because that part of the shaft is wider than the part that was cut off.
Cut the top of the rubber cover off first (at its base), then reassemble the joystick before making any cuts to the plastic. Once the plastic shaft is the length you want, then cut the rubber cover to fit.
I used an X-acto Razor Saw (available at hobby stores) to cut through the plastic, and a utility knife to cut through the rubber.
Just be sure not to cut any fingers off, because you'll need them to play games later. : )
And don't lose the little spring for the fire button, either. Those are a pain to find on a carpeted floor.
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