Performer RPM Cylinder Heads For S/B Chrysler

I had not thought about swapping transmissions, but, that could be an option. I checked out the Hot Rod blog and there is a description of what is involved in taking one of the Dakota trans and putting them in a earlier model Mopar.
Mopar Overdrive Transmission Swap - How To - Hot Rod Magazine

Since the car had optional manual transmission, would there be any 5 speeds that would fit?

As for dual exhaust and 4bbl, I would always do the two simultaneously. How much you can "flow in" depends on how much can "flow out". Once I put a 4bbl on a /6 and there was an ENORMOUS improvement in power and drive ability, however, I later installed dual exhaust and there was another noticeable improvement in power.