did you parented the empty bones (if i dont forgot is R,C,F and FRU,FRD,FLU,FLD,RRU,RRD,RLU,RLD) with ctrl+p parent and keep transformation? this is important because if you dont do it that way it will mess the animation up
If I look at it in Pose mode the parts are connected and act right if I move them but I never knew anything about "Apply pose as rest pose". I need to try to find that.
I didn't change the parenting of anything, I left the .blend like you sent it to me. Not sure I really understand how to parent the empty bones but I'll take a look.
I think that the tricks to getting the animation stuff right in Blender is the biggest problem I have. This will be an important part of any tutorial for sure.