I think you should consider getting something with a fairly "normal" layout, but a split spacebar or more thumb keys. This will allow you to use your thumb for Shift while allowing you to "float" your hands over the board and type all the other characters with the other 3 fingers of each hand (index, middle and ring). That will alleviate the use of your pinkies, so you can actually not use them at all any more for typing.
As you head to more "ergonomic" keyboards, they tend to be designed for people with full use of all fingers, but designed in such a way as to prevent causing injury in normal use. For a pre-existing injury that is not caused by typing, a normal ergonomic solution may not be ideal. For instance, the Kinesis Advantage Pro will require that you use your pinkies for some characters if typing "properly" (although you could ignore correct "touch typing" technique and move your hands a bit when typing to allow your ring finger to hit most of the pinkie key characters) and it also reduces the muscles used when typing to primarily the fingers and forearms. A normal layout board is both more familiar and easier to float around over so you can use the "wrong" fingers for certain characters.
Learning to touch type "properly" on a normal QWERTY board (keeping fingers on the home row and returning them there after every stroke) is, IMHO, going to lead to more injury down the line, even for a person with no prior injuries.
Your wrists should be as straight as possible when typing (in both axes), a slight open twist is fine (thumb side up a little, pinkie side down a little). This leads to a position with the wrists raised off of any support and hands that angle in to the keyboard so if your index fingers rest on F and J (U and H for Programemr Dvorak) then the others will rest in an arc something like AWE (A,.) and IO; (CRS), thumbs on the spacebar.
Unfortunately there are not a lot of split spacebar boards available, but the next best thing is a board with thumb keys like the ErgoDox or Advantage. I think if you adjust your technique to prevent the use of your pinkies unless / until they're "fixed" a bit, then you should be able to type well without pain.
I'm not sure a pedal will help much, it's a lot slower and requires more coordination and training to use since you have to engage the foot motor neurons as well as the hand / arm / fingers and get them synchronised. Easy enough for a drummer, but takes some practice if you're not used to it and I think it's more useful for those with "serious" hand injuries that slow down / prevent normal typing with the fingers / thumbs enough to make it worthwhile.