Interesting thread... . because I just went thru this on a marine based forum where guys want to remove the air charge cooler (it's expensive to maintain).
According to "The diesel engine reference book" (Lilly) ,the air charge cooler will increase efficiency 6% (typical) in a modern diesel engine like ours. That is even considering pressure looses thru the intercooler, timing changes due to colder air, all that stuff. It also keeps EGTs down when under heavy load (as we already know).
Also, if you look at the marine versions of our 6BTA engines, the higher hp models use sea water for the exchange medium (very cold), and the intermediate hp engines use the anti-freeze (180 F) for an exchange medium. Lower hp engines are not aftercooled.
I say the more heat you can get out of your compressed air the better.
Same with fuel temp... but that's a whole different subject!
Attention: TDR Forum Junkies 
