When I rebuilt mine I had to do the same thing- I had the thing with the ball bearings in it off center on the shaft so I had to center it on the shaft and then properly align the gears on the the sector shaft before I sealed up the box.

I'm not sure you've got to pull the steering shaft, but you most likely will have to pull the side cover and sector shaft to reset everything.

'51 Chevy 1/2 ton w/'62 261, HEI, offy, fentons, dual carter/webbers, t-5 & 12 bolt posi