I can't be the only person with this problem. I bet somebody's figured this out already. (And if "use vi" is the answer I'd consider it.) Thanks.
As everyone else will suggest, swap your caps-lock and control keys.
I also found it useful to have a single key on my keyboard that does M-x. You might already have one by default. It might look like a wavy window flag, or a cloverleaf, or a menu, or something weird.
As you have said, start to learn to use more of the special keys on the right side of the keyboard. Don't forget shift. You shouldn't be using the left shift for capital letters whose keys are on the left side of the keyboard.
You might find it useful to put your mouse on the other side of your keyboard and use it with the other hand a few days a week. It sort of trains your hands to do things differently.
You might find it useful to try a different keyboard. I've found a Microsoft Natural keyboard to be great. Your employer will spring for this if you mention that your hand hurts.
Adjust your chair height, display location, desk height, and the way you sit. Yeah, this actually affects the way you use your hands.
Don't forget to take breaks. Go get some tea or something every once in a while. I think jwz wrote a thing that periodically makes emacs force him to do that when his hands started hurting.
Don't be afraid to go see a doctor.
Good luck!
I don't type well so I don't have the proper form that might lead to the discomfort you mention but I am starting to appreciate the intuitive functionality of vim. Like I wrote, I am new to all of this so I don't have any priors or strong feelings about either editor. I find people espouse the virtues of the editor they were introduced to.
If you like emacs and it works for you, all the advice written here is helpful but from what I read, vi avoids all the crazy multi-key typing and really might be, ultimately, the best solution.
Then again, I don't know much.
EDIT:I forgot to mention, I learned Google uses the vi commands to navigate gmail and more webapps are incorporating that functionality, so it might be something to consider.
There is a learning curve, though, and your coworkers will occasionally try to use your computer and get horrified.
Note also that all the other postural changes that you can try might wind up being as important. Get a keyboard support that can be adjusted to arbitrary heights. Get a decent chair.