Back in the mid-70's someone who had been at Midwest Air Depot in OK in WW2 told me that they treated the 509th B-29's differently than the usual post-factory aircraft. While it was normal business to check the accuracy of the fuel flowmeters and adjust them accordingly, they were told that for those B-29's they had to measure the accuracy with the fuel flowmeters installed in the airplanes. That approach gave a somewhat better accuracy than the usual method of removing the flowmeters and putting them on a test bench. They wondered why those airplanes rated such special treatment, but after the war they wondered no longer.
And recall that Bock's Car nearly ran out of gas on the Nagasaki mission, so that extra precaution was a good idea.
"I assume that injection cost more than carbs and that's why the allies used it as it was "just good enough" - but help me out please!"
Fuel injection in the pre-transistor days required much more complex and expensive components than it does today, where we replaced $400 carbs with $25 fuel injection units in cars starting in the 1980's.
In addition the vaporization of the fuel in the manifold rather than injected in the cylinder provided significant cooling of the fuel-air charge. While this could cause carb icing it also could provide a significant increase in power since it gave an effect analogous to water injection.