The long thing that goes through the clutch is called the input shaft.
Did you try the clutch hub on the splines if the input shaft?
If you did and it fit, you need to measure the smooth end of the shaft, and the hole in the pilot bushing or bearing, (the bushing is pressed into the rear end of the crank shaft).
Did you use the alignment tool when you installed the clutch, and pressure plate? When you are installing the pressure plate, before you tighten the bolts, you need to make sure that the alignment shaft will slip in and out with ease and the clutch hub is aliened with the pilot bushing.
If all this will fit, make sure the transmission is in any gear, and try to slip it into place. If it doesn't slide right in, (which is the norm) you will need to turn the output shaft or yoke, (whichever your trans has) while you are pushing the trans forward. It should slide in.
It might be advisable to check the clutch spline for nicks and burs, deal with those with a file and a lot of finesse.
Hope this helps.
Ray