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A few thoughts:

A good quality trackball with super-low friction is fundamental. I've had trackballs that developed pain on my thumb, just like you stated, very quickly. These were usually mechanical. The optical trackballs can be wonderful. Both Logitech and MS make good ones.

You have to keep them clean. Again, it's about super-low friction. You should have almost no resistance to moving the ball.

Don't just move with your thumb. I developed into moving the trackball with elbow, wrist and thumb-centered motions. In general terms, I think I only use the thumb knuckle-originated motion for when accurate positioning is required, for example, while using a CAD program.

Keyboard shortcuts rule. I don't have a metric for how much I use the mouse, but if I am doing anything repetitive I figure out the keyboard shortcuts or write keyboard macros. One example is in repeating operations in Photoshop.

I learned that you need the correct posture and kinematics in order to relax. This is where my "cavity desk" worked wonders. It made me aware of when I was tensing-up almost any part of my arm, all the way up to my shoulders. If you work extended hours there's no escaping the need to learn to be very relaxed. A standard desk absolutely sucks for computer use, no matter who makes it. They are designed for writing with pen and paper and that's it. Your wrists end-up angled upwards on both your keyboard and mouse or trackball. With a cavity and an adjustable chair your forearms are horizontal, your wrist is horizontal and your fingers very naturally droop onto the keyboard or trackball. That, as a combination, is what I think make a huge difference for me and could for others.




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