Another solution is to keep the Ctrl keys where they are (note the plural), but hit them with the side of your hands: you just need to roll you hand a little bit to the outside. It takes a little practice to do this reliably, but it cures pinky pain (at least for me).

Use the hand that is not hitting the key: for C-s use your right hand for the Ctrl, and left for s. C-n the other way round. For Meta, make sure that both alt keys work, and use your thumbs: M-x right thumb and left fourth finger.

- You can't do this for C-M combinations, but they are few and far between.

- You have to have a keyboard where the keys "stick out" a little. So it does not work on laptops.

The only real issue I had was that moving around is a little slow and awkward: When going back and forth from C-f/b to C-p/n your hands are moving a lot. So I remapped C-f to C-; and C-b to C-j (and similarly for M-f & M-b) and now I can press Ctrl/Meta with my left hand and move around with my right one: bliss.