So far as I know, the most important modifications made to C-47s/Dakota aircraft were immediately postwar, when aircraft with 2-speed engines (nominally all those called C-47Bs/Dakota IVs) were "defanged" to an extent and reverted to single-speed engines (without the high blower). This was intended to improve their mechanical reliability at the cost of losing their high altitude capability. I presume these mods were made at engine overhaul depots in whichever Command they were serving at the time, and some minor mods were probably required in the cockpit to delete any of the levers previously required to manipulate gear-changing controls. However some aircraft may have been left with the 2-speed engine if they were still required for flying "the hump", but whether any were still being used on these operations is quite unknown to me, and it is likely that C-47s were by this time superseded by later C-46s, C-54s, and C-87s. Surprisingly, C-47s were supplied to most Allied air forces from 1943 onwards, despite fact that vast majority of operators did not reqire this high-altitude capability. I know that in the RNZAF in the South Pacific during 1944, various engine problems with the 2-speed engines became endemic, and was usually blamed on "sludging" of the lubrication oil. The Directorate of Repair & Maintenance (RNZAF) put it this way:
(Monthly Report for January 1946): "During the month, conclusive evidence was obtained from engines dismantled at Ohakea, that inferior lubricating oil was responsible for excessive sludging. It was found that engines with the 2-speed blower units were affected to a greater extent, and C-47B aircraft were, therefore, grounded pending removal, stripping and cleaning of the engines and oil systems. This work is is now in progress at No. 1 Repair Depot, and the grounding of individual aircraft being automatically lifted when the above work had beeen completed. Further investigation into the origin of the inferior oil revealed that Island bases were the probably source of supply, and steps were taken to to ensure that RNZAF aircraft overseas were supplied with oil from New Zealand.
(Monthly Report for February 1946): "Over half of the C-47Bs grounded in January have been returned to service after having their engines removed, stripped and cleaned at Ohakea. Remainder of work is proceeding satisfactorilly."
(Monthly Report for March 1946): "Further investigation on C-47B sludging by DSIR (Department of Scientific & Industrial Research) culminated in a report which revealed that when the engines are inhibited and stored, the carbon is gradually loosened by the inhibitor. When the engines are replaced in service, the flushing and scouring action of the circulating oil washes the loose carbon off with the result that it circulates in the oil stream, and, if not filtered out, becomes deposited on, and blocks the pressure filters.
(Monthly Report for August 1946): "Pratt & Whitney R-1830-90D engines. Following the recent troubles experienced with blowers in the -90C engines, use was made of some modification kits to modify two -90C engines to -90D type engines. This mod converts the engine from a 2-speed blower to a a single-speed blower model. Two modified engines have now emerged from the RD (Repair Depot) and are no on issue to Whenuapai (the main operating base for all the in-service C-47Bs)./