Semaca,
Can't you make a bootable DOS CD or USB key and put the dos program ATIflash along with the ROM posted above (if you have Sapphire NE with Hynix).
Boot your Mac Pro into DOS, then use ATIflash to backup your original ROM, then flash with the new ROM.
I am just remembering my steps for backup up and posting the ROM for the 8800GT Mac Edition when it first came out. Perhaps the difference is that card was already EFI capable and thus it had no problems booting to a DOS environment.
Also I don't know if this will work with two ATI cards, I don't know if ATIFlash can specifiy which PCI-E port you want to flash etc. so if you have two ATI cards I guess it could be problematic.
BTW, much thanks to Peloche for posting the ROM above. I will test it out when I get home later tonight and report on my findings.