I had exactly the same problem. Heavy tendinitis in my right elbow, mostly due to a regimen of squash, badminton, and rock climbing multiple times per week.

I similarly switched to trackball mouse and keyboard without num pad (I was already on vim).

But what helped me more than anything was a keyboard tray that goes below the desk, almost on your lap.

Whenever we move offices at work, it sometimes takes a day or two before the tray is installed and I notice that the discomfort starts coming back quickly.