I'm not a hand quilter, but I can't see why you would consider continuing with a method that causes you pain. Have you considered machine quilting? You can always quilt in sections (Marti Michell's book Machine Quilting in Sections is good at explaining various options) if you're worried about putting a large quilt through a small machine throat.
This isn't to discourage you from hand quilting (which I admire) but just to point out that there may be other options.