You need an alignment tool to fix that, they can be bought at any auto parts store.(cheap) Or if you have an old input shaft from another transmission just stick it up there and have someone press the clutch, then move it around and you will feel it slide in place. Release the clutch, Pull it out and put the transmission back in. It's easy.If you buy one make sure it has the coarse splines ( the same as your transmission).
If you can't find one, Get a piece of wooden dowl or a punch, have someone press the clutch and move it around, eyeball it as close as you can, put a tiny bit of grease on the end of the trans. and put it up there move it around it will go in place.
