Well now's your chance to first of all make sure that the box is centered while it's disconnected. Unless you did that before removing things, and know for a fact it did not move, I would do it again.
Then with the steering wheel straight, see how the shaft lines up. This "should be" the way it was before.
But even without that, generally you want the set screws to engage something other than splines. Whether it's a full groove where the old through-bolt went, or just a flat spot, I would use it if it lines up properly with everything else.
The bottom line is that you want the box centered and the wheel straight. If you need to remove the upper joint and re-orient it on the splines too, to get this done, then so be it.
If you find the need to put a dimple in the shaft to give the set screw a place to land, be very careful as the shafts are hollow and many a steering box input has been buggered from too-deep dimpling for steering shafts.
The fact yours was on before should mean that you will have something workable already. Which is most likely the flat spot you mention. All that other stuff I said was by way of "just in case you run into this" scenarios.
Good luck. And if in doubt, post up some pics.
Paul
