Some engines that were originally paired with an automatic transmission may not have the pilot hole fullly machined.
Do you have a pilot bushing, or the roller bearing that fits into the convertor recess? It could have had the roller bearing pressed in and appear to be "stick ready", but not have the pilot hole fully machined and your input shaft is bottoming out in the crank. You really need to check the depth as
@67Dart273 outlined above.
Hopefully, all you're experiencing is a little stubbornness of the splines and pilot to mesh together. They can be finicky sometimes, keep at it.