I know nothing about warbirds, but I guess a lot of the operating costs would depend on how ubiquitous the aircraft was in WWII (correct me if I'm wrong). The DC-3/C-47 was produced in squillions and is still operating today so I'd imagine keeping one in the air would be relatively (stress 'relatively') cheap. I inagine also that aircooled aircraft would be cheaper to maintain and run than liquid cooled.
How does the Yak-3 replica stack up? Are Allisons cheaper to run than Merlins? Is the wooden structure easier to repair than aluminium?
A DC3 is still horribly expensive to operate, for a 30-odd seater. And given that there isn't much comparable being flown, the term 'relatively' doesn't really work.
As far as aluminium vs. wooden structure repairs, aluminium is easier to repair, and the skills required to effect such repairs are more readily available now.