Before anyone says "Do a search!", I have been searching for days and can't find anything that helps.

Problem:
I can't seem to get my steering wheel to line up correctly after rebuilding the gear box.

Backstory: I rebuilt the leaking steering gearbox on my '89 Formula for the first time and the steering wheel was straight when I put it back in. However, one of the seals got torn when I was assembling it and started leaking, so I had to take it apart to fix it.
When I put it together the second time, the steering wheel was about 15-20 degrees to the left (about the 10-10:30 position).
The pitman arm was perpendicular to the vehicle as it should be, but the input shaft wasn't straight.
Isn't there only one way it can go in?

Last night I took it apart again and reassembled it according to GM specs (except for the torque specs, I guessed on those because I couldn't connect my torque wrench to the input shaft. Is there a special tool for that?), and everything seemed lined up when it was on the bench.
But once I put it on the car, it was still in the same position as before!

I don't know how it went together right the first time, but not the other times. I must be making some mistake. I've rebuilt several Ford and GM gearboxes and never had this problem. Can anyone help me?

Thank you.