I am resistant to using Viper mode as I think it will mess with the key bindings in the 20 some odd major modes I use every day. So I am going to try something else. I am deleting the Ctrl and Shift modifier keys from the X key bindings on the left side of my keyboard and will force myself to use Shift and Ctrl on the right hand side for a while. Spreading the wear out over both hands should help things a bit. Of course things are complicated a bit by the fact that this Mac keyboard doesn't have a left control at all. No biggie with xmodmap. Just use xev to figure out what keys send what code and make a xmodmap input file like this.
clear controlOh yeah, if you are using Ubuntu or probably any mainstream distribution, changes to xmodmap are often times intercepted on startup and different key mapping utility is used. in short, make this file as xmodmap in your home space, apply it, then restart the X server. You will probably get a dialog asking you if you want to include these key mappings or not.
keycode 50 = Shift_L
keycode 62 = Shift_R
keycode 37 = Control_L
keycode 108 = Control_R
keycode 64 = Super_L
keycode 134 = Alt_R
keycode 133 = Alt_L
add shift = Shift_R
add control = Alt_R
add mod1 = Alt_L
add mod4 = Super_L
Just run xmodmap <input-file> to effect the changes. Also, I am going to try and mimic the key placement of the older space cadet keyboards, which were made for Emacs. The Wikipedia page states that a big difference was that the space cadet keyboards had modifier keys in a "thumbable" position. So I am leaving my left Alt as Alt and setting my right Alt as a Ctrl. This means that in a few weeks time I should be using thumbs for most Emacs work (and everything work, as xmodmap changes are X global).
Now, the only thing I use my left pinky for is typing and Tab, which seems fair. I'll see if things get better. Maybe I will end up in Viper mode.
Update: Things did get better, but just barely. I do believe that the numbness is caused primarily by just a few common Emacs commands, like C-c C-c, C-x C-s, or any command that uses the C-c or C-x prefixes. In fact, my opinion is that the left hand is way over used in Emacs. I had to re-enable the left shift key for the sake of my typing speed. This has also revealed that Apple cut a few corners when it came to their keyboard hardware (everybody does). The left and right alt keys, when pressed at the same time, will stop any keys on the "zxcv" row from even producing key codes, so that's a pain right now. As of testing just a few minutes ago, the numbness comes back with just a few minutes of typing on a normal keyboard layout.
Update (after a few months): This has basically been resolved. A few thoughts: mapping to thumbs seemed like a good idea, but thumbs get worn out too. After a few months, my thumbs were pretty ache-y. In the end, the two things I found that really did make a difference were: 1. binding caps-lock as a control and 2. switching to a Dvorak layout, more specifically the Programmers Dvorak layout, which I think is pretty smart. I can't say how much each of these contributed individually, as I changed them simultaneously. I plan to write a post on Programmers Dvorak soon but suffice it to say, switching layouts isn't a decision to take lightly. The caps-lock thing, on the other hand, is dead simple and helps tremendously; I very much suggest it. I only wish I had another key right beside the caps-lock (or in the pinky position on the right hand) that I could bind to Meta/Alt.