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OK, I think I would agree with "rwgregory". If you didn't, you should be able to rent a pilot shaft tool or clutch alignment tool at your local parts store. Use it to line up the clutch with the pilot bearing.
http://www.clutchtools.com/ . If you have already done this then I think you may not have the input shaft lined up with the pilot. Sometimes you have to lift up on the front of the tranny as well as the back while installing it to line up the pilot. If this doesn't work let us know, there are a couple of other things that could cause this.
LockDoc