When the VB goes back in the rod sometimes tries to push the lock (pawl) over but there is a tooth of the gear in the way at the moment so you have to turn the driveline (or output shaft) so that the rod can go in where it belongs.
Any of that sound familiar?
Heck it's even possible the linkage is not allowing the trans to go all the way into park.
Have you verified the linkage isn't stopping it from going all the way into park at the trans?
On the pumping fluid problem, what has changed since it was working? (converter)?
