I've upgrade my Mac Pro 1,1 to 2,1 with the original CPUs (2 duo core 2.0GHz) inside. The new CPUs will arrive in August, and I can't wait until then.
No problem at all.
Just follow the instruction in the below video. This is the newest instruction so far. I followed this video to flash my Mac Pro.
You will need another device to view it step-by-step.
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I don't think you'll need firmware 2,1 to run El Capitan.
But anyway, it's easy and cost nothing to flash the firmware.
Just flash it then upgrade to El Capitan.