Hi,
The info on that page is confusing, and I am not sure which step to begin at. Here is my present state - the hard drive is pure GPT, and on one partition Win 8.1 is installed in UEFI mode, and in another partition, Yosemite has been installed. I used the image file from Olarila on piratebay to make the pendrive.
I can boot Yosemite from the pendrive. Following the instructions on that page you linked, I copied the EFI folder from pendrive to Yosemite partition on hard disk. I entered clover from USB stick, and the option I had was "Add all Clover options", not "Add clover UEFI options". Anyway I added all the clover options, so at bootup I get several legacy and UEFI options. Here is what I get when I boot:
1) If the pendrive is not in the USB port, when I select "Boot from UEFI Yosemite", it simply shows me the manufacturer logo of the laptop, and boots into Windows.
2) If I keep the USB stick plugged in and select the same option, it starts to boot, but encounters a kernel panic and restarts.
3) If I keep the USB stick plugged in and boot from the USB stick, then as before, I can get into Yosemite.
Obviously, I want to be able to boot into Yosemite or Windows without the pendrive. Please tell me if I have done something wrong.