Repairing permissions won't do anything on ElCap.
It's already done. A number of people in this thread are the living proof.
My little theory about your problem: "?" folder issue seems caused by sandboxing.
After installing ElCap on a supported Mac add "rootless=0" to com.apple.Boot.plist, next replace boot.efi and put the disk in 2006.
Hey guys, I wanted to report that I got El Cap running in my 1,1 last night.
I listened to this guy and got it running easily.
1. I had installed DP1 on a 4,1.
2. From a working Yose install on the 1,1 I accessed the El Cap disk and replaced the boot.efi files. (tricky but doable)
3. I used a text editor to add "rootless=0" in the apple.boot.plist in El Cap
4. I rebooted into El Capitan on the 1,1 !
5. I ran the pikeryosefix app.
6. I ran all of the updates right from Apple Store, right to DP7.
In retrospect I probably could have run the pikeryosefix in the 4,1 and saved myself some bother. I just posted in the Yosemite on 1,1 thread that the value of this app has been overlooked. If you think about it and use it at right time, you don't have to do the manual replace, just run the pikeryosefix app while on a El Cap capable machine. Reboot until it won't boot anymore, this means the 32 bit EFI is in. Move drive to 1,1 and enjoy.
The point is, I read these threads and see a lot of people have a lot of trouble. It is easy as pie if you REALLY think about what you are doing and why. Thanks to Tiamo, Piker, Hennessiee, and Blacksheep for their hard work. No other 2006 era Mac can so effortlessly run El Cap, in fact most can't at all. The cMP may end up being best Mac they built.