Slant 6/904 flex plate no longer fits on new motor

Doesn't look like you've got the pilot bearing totally out, the register needs to be empty for the convertor nose to fit.
And here's another "heads up" for you- the convertor snout on your '64 904 will be too small in the later crank's register. You'll need an adapter bushing to ensure the convertor is properly centered and supported.
Was sold by Pat Blaise Transmissions, but he may have retired... his Ebay user name is torqueflight patty.
They are (or were?) also made and sold by member @Charrlie_S