When you did this clutch, did you change the flywheel? Did you use the centering bearing on the flywheel? If you did, you may want to remove it, make sure it fits the input shaft on the transmission.

I have dealt with this from time to time and you have to get everything lined up just right to get it on easily. If you have the engine and transmission out, you can try laying the engine on the timing belt cover side with some blocks of wood to hold it steady, clutch side up. Then, lay the transmission on top and wiggle till it goes all the way on. If it doesnt go on this way, then there is definetly something wrong.

If you are out in Valrico I could check it out on Sunday or any evening during the week. I don't mind.