Transmission

did you use a clutch disc alignment tool when installing the new disc? if not the disc may not be in alignment, so the trans input shaft wont go all the way in

oldcarpenter is correct. Without that tool, it's possible but quite difficult. The shaft hole has to be dead center

You can buy a plastic alignment tool for just a few bucks at your local auto parts store but they are worth their weight in platinum.

I'm pretty damn sure your clutch disc in not aligned....get the tool....and re align the disc....