When you say you followed these steps... there is a different method for installing El Capitan and mixing the two doesn't work. Issues with SIP in El Capitan mean the same method doesn't work as it does with Yosemite. I have successfully installed El Cap onto a fresh HD using the "Pikify" script created by RTHPJM and it worked fine. I always install onto a new HD or SSD so the original OS is untouched - then if any problems, I can boot back into previous OS. Were you previously running Yosemite with PikeYoseFix? If so that may still be launching causing some of the issues. The El Capitan thread has a lot more useful info that will help.