Your correct in questioning the position of the shifter and the bench seat. I have a 50AD 350 SBC with a Saginaw (only difference in the shifters is the reverse rod) and ordered a custom Hurst shifter from "Patricks" who makes a custom shifter mount that bolts on to the gearbox and not the tail shaft. It moves the shifter forward to the proper position. He also has the perfect fit floor pan and boot to fit the set up. Its about $350.
http://www.patricksantiquecars.com/chevy-gmc-auto-parts.html