Is there a mopar engine and trans compatibility chart somewhere? You know displaying what trans' changed throught the years and what bolts up to what.
Check out ForwardLook.net ... they (we) should be able to help you out there. I know from experience that you can't mate a '66 318 to a '60 trans, and you can mate a '61 413 to a '60 trans.... but I'd be going from memory if I went any further... and that's never a good thing. Do you have a specific combo in mind? That might be the best way to approach it.
Try these http://1962to1965mopar.ornocar.com/techstuff.html http://www.autohobbydigest.com/t_blockid.html
On 60's and up model stuff, it's /6, SB or BB-hemi. Not sure on the flattys, but the motors (within the lines) were mostly the same for years. New hemi bolts up to SB trans. Early hemi is similar to SB, but needs spacers (different crank depth).