I guess that I have to disable SIP and then rebuild the prelinked kernel, but I don't know how to do it. I can manipulate files from my working installation, but I don't know if single user works on the El Capitan installation.
I don't see any reference to FakeSMC in your verbose boot. Did you remember to use injected kexts with your boot loader or install FakeSMC in /Library/Extensions?
If the PLK in El Capitan is corrupt, you can rebuild it easily from Yosemite....
1. Boot into Yosemite with kext-dev-mode=1
2. Open terminal and type the following lines, followed by <Enter>. My El Capitan volume is named "El_Cap", so change if yours is named something else...
sudo -s rm -f /Volumes/El_Cap/System/Library/PrelinkedKernels/prelinkedkernel touch /Volumes/El_Cap/System/Library/Extensions kextcache -u /Volumes/El_Cap exit
3. Reboot into El Capitan .Go to the full post