John,
Have you called Classic Parts for assistance? As you know, the heater you bought is an aftermarket heater assembly and its parts are different from either of the GM optional heaters available in 1953. The outlets/ducts that came with the Classic Parts heater are (from what you describe) different from the outlets/ducts that are used in an original heater set-up.
By the way, the original ducts for recirculator and air-flow (fresh air) GM heaters were the same in the same years, but they were different from year to year during Advance-Design years (probably different in 54/55 due to cab/windshield change but might have been different 53-55 due to a change in fresh-air/air-flow heater?). None of the information in this paragraph is pertinent to you - Classic Parts should know how their ducts/outlets should be installed/orientated.