Did you compare the new pilot bushing to the old one removed to be sure they were the same thickness? A thicker bushing might prevent the input shaft from settling all the way in.
If they were the same thickness, perhaps the new pilot bushing didn't get fully seated in the crankshaft? That might keep the input shaft from sliding all the way in.
Alternative thought. Did you by chance replace the input shaft in the transmission? If yes, did you check the fit of the shaft with the new pilot bushing?
Just some random thoughts that might be related to your problem.
