Later model Y engines transplant into the 1954 U.S. engine bays without issue when used as complete engines and are simply replacing the existing 239 or 256 Y engines.  The external dimensions, motor mounts, and bellhousing patterns are the same for all years of Y-Blocks.  Internally and accessory wise is where the differences are though.  The ’54 engines have their own oil pumps, water pumps, fuel pumps, camshafts, distributors, and timing covers that do not easily interchange with the 1955 and up engines.  You also have to be careful of the pickup and truck engines for the various years which can also exhibit some additional differences in the oil pans and water pumps.