Could be bad news. You may have ruined the bearings in the torque tube. They make a special tool for this, it's called a clutch alignment tool, or a pilot shaft tool. Did you use one? If not, spend the few bucks to get one.
It can be a pain in the rear to get them aligned properly. But, I would move the torque tube back, and spin it to see if the bearings in it are O.K. Then i would look at the pilot bearing to make sure you didn't damage it either. It will take awhile to disassemble everything to check, but it's still better than if you got it all back together.
ScottR's idea works great too!
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