OK, not sure why I can't update firmware. I pulled out a Mac Pro 4,1 (still had 10.6.8 on it) and went through downloading the 5,1 EFI, then opening it to mount the image, then ran the 2009-2010 update utility.
Everything goes great. Creates the RAMDISK, copies the files over, finally comes up with the dialog box to shut down and then instructions to hold the power button. So I shut down, wait for the complete turn off, then turn back on, holding the button until the LED flashes. I hear the tone, and see a grey screen with apple logo and progress bar, but I don't ever see the progress bar actually do anything. After a bit, the Mac reboots and lo and behold, I'm still at 4,1 (according to system report). Did it three times, each time doing the same thing.
My boot ROM is MP41.0081.B04.
I've removed all the old hardware (RAID card, fiber channel card, drives) but left the video card, and popped a single SATA SSD in one of the bays, and installed a fresh El Capitan. Copy over the files to the DOWNLOADS folder, mount the EFI image, run the upgrade utility, everything goes great. Shutdown...power on, hold the button, wait for tone, but now I just get a normal boot. The grey screen looks like the normal boot screen. Again, still MacPro 4,1.
I figure I'll try updating to MP41.0081.B07, so I obtain that utility from Apples web site, run it and it says that the firmware cannot be upgraded and that it could be because I'm not booting from a drive with a GUID Partition. Problem is, my partition IS GUID Partition Map (according to disk utility).
Could it be the SSD? So I put in a single HDD, boot on my El Capitan installer, disk utility and erase the HDD making sure I have GUID Partition, reinstall El Capitan and try the whole thing again. SAME ERROR, that the firmware cannot be upgraded and to make sure that my boot drive is GUID.
I figured I'd give the 2009-2010 utility another go with the HDD installed, but same thing...upon reboot after holding power button and getting tone, the Mac does a normal boot up and no firmware progress bar screen is seen.
What the HECK???
What else can i try, or does anyone know why I can't upgrade? BTW, the CPU is original quad core 2.66, and video card is stock nvidia.
Ideas would be greatly appreciated. I've spent (wasted) many hours getting this far and still have no joy.