While I don’t have an EXACT solution for this, which I apologize for in advance, a couple solutions I might know are to either: Add a rootpart or some sort of other root, which I believe you may have already used. Or said rootpart is not big enough.
(You said it caused deformations beforehand, if you could elaborate on how your rig works when it DOES have a rootpart, that would be nice.)
Most I can make out of the top bone not animating is just that you need something to make IT animateable instead. (Refer to aforementioned rootpart.) If you still need help, let me know.