There's some pretty awesome suggestions in this thread already, but I thought I'd add a few more that I've seen have been helpful for people!
- Speech recognition: It's sorta been mentioned, but this is a common way to get inputs into your PC. Might be a good candidate instead of typing messages in game as well
- Macros to keys on your mouse: Autohotkey is the one that I've seen used most often, you can bind certain messages to the mouse and use that as a quick way to relay things
- Windows On-Screen keyboard: I'm sure there's Mac equivalents - some players use this for certain key functionality that would be difficult to bind or if they already have a lot of things bound. It's not great for if you want to type in game, as you keep refocusing in and out of the keyboard
- Pedals/other physical simple inputs: There's a lot of devices that are simply just a single button or clicker that you can tap that can provide a signal. Arduinos or raspberry PIs are one of the easier ways you can take these inputs and then have it translated as a specific keyboard or mouse output, most of these you can connect with USB or microUSB cables directly to your PC. JoyToKey is one of the things I see people take advantage of in these cases
As a side note, and I'm sure your physical therapists may be better knowledgeable, but you may want to consider getting a mirror box if you start experiencing phantom limb pain while playing to help relieve some of it. I'd expect a lot of the reactionary nerves that have built up may become a bit grumpy. Can probably set one up on your desk right below your monitor :)