The input shaft on my tranny sticks out past the tranny bellhousing
That's not a good thing....back to the rebuilder you go. Take your converter with you and have them, after putting the input shaft back correctly, install the converter and make sure it seats properly as well. Folks who don't secure input shafts (there's a friction cap which covers this area, holds the input shaft in place and protects the pump cavity from dust during shipment) sometimes install pump gears backwards too, which makes installing the converter a bear.
Don't mess with it yourself; take it back to the rebuilder and get their assistance. That's what you paid for.