As others have said, use the clutch alignment tool to make sure everything is positioned properly. After that, get ready for lots of wiggling. Not only will you want to try moving the back of the transmission up/down and side to side, you may also need to rotate the transmission clockwise/counterclockwise so that the input shaft's teeth can properly line up with the clutch disc.
One last possibility, though it is unlikely: did you check to make sure the clutch disc physically fits onto your transmission's input shaft? I once tried installing a new clutch in my former Shelby CSX, but it would not go together. I finally took the clutch back off the car to inspect it, and that's when I learned it's center was too small to go onto my transmission input shaft! I had to get a triangle file and spend a couple hours expanding the threaded hole until it would fit (it was a custom puck clutch, so I was dead set on making it work).
My fleet: 91 Miata, 98 Wrangler Sport
, 01 Suburban 8.1L, 14 Impreza, 03 Protege
Jeep mods: 4" longarm + 1" BL, 35" KM2s, 4.56s with dual ARBs... and lots of scratched armor