It does sound like he did have some damage that was caused by a surgery made too late. It is just at times or does he always exhibit signs that he cannot move those limp parts? Do you think that maybe it is because he wears out quickly?
His equilibrium is most likely upset since he had this problem. With the absence of the fluid, maybe it will take him time to adjust.
I think also that since he has been through quite a trauma, you might want to give him time for his brain to recuperate and adjust to being normal. His brain will continue to grow, so it is possible that with a lot of work you can train him to use other parts of his brain for the possibly damaged ones for his mobility.