Since this thread came up near the top of a google search, and since I've done it before, I thought I would chime in just in case someone else looking for info sees it.
My Pro 1,1 with 32GB RAM, an SSD, and an ATI 5770 runs El Cap absolutely great. The only big issue is that it uses quite a lot of power compared to a modern machine. No, it's not as fast as a new mac, but it's totally capable of being a daily driver for most uses.
You can NOT brick your machine doing this. All you are doing is booting from a slightly modified El Cap install. There is no need to upgrade your EFI to the 2,1 roms unless you will be upgrading your CPUs. There is no need to flash your video card's ROM to a mac version. You will need a more recent video card--I use a 5770.
The process is simple. Install El Cap on an SSD/HD using another mac that does support El Cap, disable csr, and then change the boot.efi file to an alternate ( https://github.com/Piker-Alpha/macosxbootloader ) optionally using a script to make things easier ( https://github.com/ryanmaclean/Mac-Pro-1-1-El-Capitan-Upgrades ).
If your video card isn't a mac version, your screen will be blank (no boot logo) until your desktop comes up, but that's never been an issue. You may need to fix the boot.efi file after an update, but I don't imagine that happens much any more.
Other than that, enjoy!
Both my ati 5770 and my nvidia 660ti work on my pro 1,1 with ElCap. While it is true that older cards wont let you boot and only suffer a few seconds of blank screen, it is not due to a lack of EFI bios on the cards. There isn't an EFI bios available for any 5770 afaik, and Zotac was not kind enough to provide an EFI update for my particular 660ti. I am sure of this due to working through these issues getting PCI passthrough to work with KVM/qemu with these cards on another box and having to substitute an EFI rom via a file. But, yes, if you have a pc/win card older than 2012 or so, you might need to flash for mac or find a more recent card.