It forced me to either move the keyboard too far to the left or the mouse too far the right, the former causing wrist pain in both hands, the latter causing pain in the right wrist.

So, what fixed my pain was the smaller keyboard, not the lack of a numpad. The numpad just happends to be a big, expendable chunk :)

One of the keyboards I got in order to fix this was a Microsoft ergonomic keyboard, which includes the numpad and is also wider than what I've used before. So getting an ergonomic keyboard actually made things worse in one case.