I think there is a new means to disable this via a preference pane. Not 100% sure, I haven't played with El Cap much yet.
I did have one thought on the USB issue, probably not related but a thought. I was helping a guy run Yosemite on his 1,1 Mac Pro and he had lost his USB. It turned out that the ancient BT card no longer had a driver (Atheros I think) Since BT was plumbed via USB, the lack of a driver buggered up 1/2 of the USB ports. The fix was to physically remove the BT card and replace with a Broadcom one, then ports came back. This is probably a different problem but I thought it was interesting that we had experienced a USB issue before that was easily solvable.
UPDATE: Got it running on my 1,1 yesterday. Super easy, I did the install on a 4,1 then moved drive and did surgery on 1,1.
See the El Cap on a 1,1 thread in MP section.