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Take it back apart and inspect the pilot bearing. Never put a bolt in it to help line it up or pull it together. I would reset the clutch with your alignment tool. If you are using the plastic one it will flex down with the weight of the clutch. Support it and then eyeball it to make sure it looks straight. Once everything is lined up right it will push together all the way. As stated above if you do not support the front of the engine it will rock down and make it more difficult to install.
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