Best theory I got:
The center hole in that one spring was egg shaped and it shifted a bit when pin was driven back in.
Best plan I got until someone hatches a better one:
C-clamp leaves together. Drive out center bolt. Place stack in vise and try to re-align the stack. Drive new center bolt while stack is clamped from sides in the vise. Maybe try to tighten tip the leaf clips/clamps somehow. (Could definitely use some pointers on that process).