If it stopped about 1/2" from all the way, it's probably the pilot bushing isn't exactly lined up and the trans input shaft isn't able to go into it.
I've had many experiences with just that sort of thing, even when you use a line-up tool.
If you can get someone to push the clutch pedal down it might go, or if you
don't have any help, you can leave the pressure plate bolts loose (just snug, so the clutch disc can move a little) and you might be able to get it to go all the way. Of course, then you'll have to take the trans back out and remove the bellhousing so you can tighten the bolts, but it should still be able to go in afterwards.
Or you could try pulling it in gently with the transmission mounting bolts.
That's what most people do.