If it's the steering shaft from the column to the gear box that you're talking about, and they won't line up properly, the obvious question is did you put the key in and unlock the column so you can turn it to line it up? After that, compare closely to the original box and make sure any flanged shaft adapter on the original was swapped over to or matches the new gear box. Sometimes the simplest swaps become a real pain over the smallest details or seemingly insignificant missed step that even the instructions overlooked. Hope this helps if even a little, and don't give up.
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