Just sold an '02 FZ-1, simultaneous w/purchasing my Bandit. Knees don't give me much problem, so I can't say I'm real focused on that, but the bikes seem similar to me, perhaps a bit more room on the 1250S.
I'm told that the Bandit seat is adjustable for height, is typically delivered set in the lower position. I understand it's not a quick change, suggestions that you might ask your dealer to effect it, but that would provide a bit of extra legroom. Perhaps just enough to make it livable.
Garth