An inch or so...maybe a bit more is the depth of the pilot bushing and the input shaft stops before it gets all the way to the bottom. If you're out by 2+ inches it makes me wonder. But I know something is being struck on the way back in. It is just hard from this point to say just what it was. If I visualize a side view of the 3 speed, you've got the pilot bushing section of the input shaft...and that as I've said is an inch to inch and 1/4 or so. Then you have the splines that engage the disc and those are maybe 3 to 3.5 inches in length. Then you have the clutch gear bearing retainer piece and it is maybe the same length as the splines. Nothing really is 2 or 2+ inches that catches my thoughts. If the splines start in the disc, they're going to slide all the way. If the shaft goes in the pilot bushing, you can always wiggle or wobble the transmission a bit to get that in and the only thing left might be the clutch gear bearing retainer hanging up on the throw-out bearing. Did you change that bearing or has it come off of the fork?

~ Jon
1952 1/2 ton with 1959 235 | T5 with 3.07 rear end