could Darwin be built up any to maybe act as a second port for the Eastern Fleet?
Short answer no following reasons:
-Darwin would require massive investment of both civil and military infrastructure on its port and infrastructure as practically everything had to be brought in by sea. Just look at the design of the Darwin pier (a dogleg!)
-This means less money for investment elsewhere.
-It is to easily isolated from the rest of Australia by land. Even if the Commonwealth government got behind the QLD gov and built the missing link railway from Dajarra to Birdum or behind the SA gov from Alice Springs, it would still be a massive undertaking, never profitable and very suceptable to the elements in the rainy season. For the QLD option, this would mean upgrading the Mt Isa line so that it could take at least a C17 locomotive and at least 10 TAL (something that wasn't done until the 1950s).
-Belief in Singapore as the lynchpin for defence
-The geographic location of Darwin. Its to far away from key points in the Far East to make a decent alternative location for the fleet.
-Somehow change the Australian governments view on defence spending in the 1930s
-All weather defence roads into the interior as touted by Forgan Smith in 1939 - however I doubt they would extent to Darwin without commonwealth money (which wasn't given anyway).
There was a very good thread about this some time ago about this.