Based on what I know, those three aircraft were 41-2440 Calamity Jane, 41-2632 Crock O'Crap and 41-2658.
Gene Salecker's book has an interesting tale about how 41-2440 got her nickname. According to a 394th mechanic, Phil Klingensmith, when the three B-17Es reached Fiji they shared the airstrip with Navy planes from the carrier Saratoga. One evening three Navy planes were taking off and dust stirred up by the leading aircraft caused the two following planes to go off the runway and into two parked B-17s. One of them was 41-2440. A repair team from the Hawaiian Air Depot was flown in and 41-2440 was repaired using parts from the other, more seriously damaged, aircraft. That was late November 1942, and the repaired plane was given the name Calamity Jane.

It also seems to me that 41-2658 is the only logical contender as the aircraft that was damaged on Fiji and then cannibalised to repair 41-2440. All others are accounted for one way or another. I think the fact that 41-2658 was written off on June 15, 1944 supports that theory - I believe that's a "blanket" date used when the records were brought up to date.
Can anyone fill in the gaps?