By any chance is the flex plate installed backwards? I need to take a better look at the pics....
The flex plate has two large open 'window' cutouts, and the third 'window' has a plate in it, so that is your balance. Sometimes there are some partially drilled holes to fine tune the balance.
'64 to '66 cranks are the same, '63- earlier are different for the Dynaflow trans.
Flywheels and flexplates interchange within specific engine families..... 64-66 401 and 425, a 300 flywheel will interchange with 340 and 350.
401 ST300 flex plates have two sets of holes for converter mounting so they can be mated to either the smaller Skylark GS converter or the larger converter used in the big cars. Some other 401-425's have the dual pattern as well, I think 65-66 only?