I'm not sure if you saw this or if it appliesto you but the same firmware (v 2.40.5048) appears to be available through some sort of windows installer here: Mellanox ConnectX-3 Firmware Update v2.40.5048 for Windows - USI wish it were the binary firmware file, but according to the IBM instructions where I downloaded it, it is to be executed in some proprietary software to perform the update. mstflint does not recognize it. Peaking a little at the .bin file, it is an executable, not a firmware image.
Also, since I'm only being initiated into this I was wondering how much card revisions matter? I believe Stereodude had a 00D9691 part that was Rev A5. I also have some IBM cards but they are 00W0054 parts with Rev A1.
I can crossflash them using the generic firmware available for the CX312A-XCBT but it specifically says A2-A6 so I wasn't sure if this means I'll run into problems later?