After much fiddling, luck and timing finally came together. Avastar just put out a test version that allows more fiddling with quadruped skeletons. This makes it easier for me to experiment with the rigging in Blender, and if that fails, to bring in Maya animations and then work directly from it.
An interesting note: just for S&Gs, I imported a COLLADA file of my horse from Maya. No surprise, but the hip bones are turned. The annoying thing is, I did what I could to fix them in Maya, suspecting that was the case. It might be that Avastar, being designed to work with SL, is just going to be more efficient at not muffing up the skeleton.
The other annoying thing about the turned hip, is that I used the provided SL to Maya skeleton without any rotations or imports. I know because I double and triple and quadruple checked my procedure on this. Why it resulted in a turned hip I cannot say but clearly it’s the culprit behind the weird hip animation troubles, as I suspected.
Onward and upward!