It took quite a while because I was busy with other things and because I tried to do too much at once. Once I broke the problem down into smaller pieces, things quickly fell into place. I had to rewrite most of the underlying bones and joints but I eventually got the skeletal animation to work with actual graphics. Here's a half-sized Galamoth from C:SOTN.
I completely got rid of bones and just use FlxSprites now. Each FlxSkeletonJoint is responsible for how the parent and child are positioned relative to each other. Joints do this by attaching the "ball" point of one sprite to the "socket" point of another at a given angle. Each joint can still have it's own set of animations. The FlxSkeleton itself just holds the bones and joints and helps assemble and detatch them.
Next is basic inverse kinematics - just enough to support things like "look at that" or "put your right hand here". That should be good enough for what I need.