From what I've found messing with fwd cars is that while your 'trying' to get the trans up and in, the input shaft doesn't make it in the disc enough to align it in through the flywheel to pilot bushing and usually while your grunting and trying to get a better grip the trans gets let down a bit, the input gets angled and pushes the disc over to one side, over powering the grip of the clutch and mis-aligning the hole and jamming it.
I've seen peeps get it 'so-close' that they think that just popping the bolts in and tightening them will bring it together and it will all be rainbows and bunny rabbits.. All to bust an ear off or crack the trans case.
Pull the trans again, get your alignment tool back in and see if it just slides in or it gets jammed also.
Check the end of the input or Pilot end of shaft. Is there a burr on it? If so, file it off smooth.
Just my .02
"life without God is like an unsharpened pencil. It's got NO point"