Didn't they supply a nut and washer for the new box?
I'm fairly certain they should have...
Who knows what shaft went back in, I guess that depends on who actually rebuilt it and what part of china the parts came from.
Maybe take it back to napa and have them set you up with what it requires.
If that's a no-go and depending on your area try Harry's Steer & Gear on Groesbeck, near 14 mile.
They're just south of the old Mancini location.
Good guys there, on a friday at closing time they rebuilt my 1.06 federal steering pump in an hour for $60, including a granaded valve that needed replacing.
If your not too far from them you still have a little time before they close, and look... it's friday.