If the powerhead is a 1954, then it likely has been cast to receive an identifying welch plug, but will not have a plug. At least that’s been my experience. If you try to put a 1956 or later powerhead on the 1954 or 1955 motor, then the starter mounting bosses will not fit to your 1954/1955 starter housing. The 1956 and later have a totally different starter and flywheel. Different base gaskets also pose a problem as fleetwin mentioned.
Regarding the cooling issue, if all of the passages are clear, grommet is in good condition and not partially folded over, pump, key, housing, and plate are in good condition, then the problem could be sealant partially blocking off the water passage, again as fleetwin mentioned.
There is one other thing that can go wrong during assembly, and it happened to me. Part 41, 30339 Gearcase to Bearing Housing Gasket was installed with a light coating of gasket sealer, on a 1954 Johnson 5.5. When installing the water pump assembly and housing, the gasket rotated slightly thereby partially blocking off the cooling port opening in the gasket. I didn’t even notice that the waterpump housing screws were misaligned to the gasket, and they were easily forced through the gasket, and made there own holes. This was a valuable lesson, and ever since, I always use alignment pins when installing the assembly and housing.
Improvise-Adapt-Overcome