I also have certain RSI-like issues, but I think mine are caused by mouse clicking, not keyboard usage. These days I'm using an extra numpad on the left of the keyboard with certain custom actions attached (see my AHK file on the website). So I can still move the cursor with precision, but don't have to click anymore.
I wrecked my right wrist using cheap traditional mice. Its not just their bad ergonomics, the buttons on the cheap ones are stiff which can cause muscle strain. A few years ago I switched to my left hand and got a Kensington Expert Mouse (its a trackball) and so far no problems.
Have you seen this? It's a vertical mouse designed to lesson the strain on your wrist.
Yes, I looked at that one and all kinds of strange shaped ones when I was researching it and found a flaw in all of the designs. The problem with mice in general, its not just the angle, its the fact you have to move your entire arm just to move the mouse, so its physical location is always changing. With a trackball it never changes location, you just move your hand over it. Even with the trackball, I take care to rest my finger tips on the ball and my thumb on the pad so my wrist remains straight.