So, I'm going to post how I managed this, because I think some folks need a guide to follow especially once they manage to get a Clover USB bootable disk working. Of course, that is the key. The best thing you can do, if you want to move from Chameleon to Clover is to get that working.
Yes, this is the guide you want to use:
http://www.tonymacx86.com/basics/171680-clover-basics-switching-advice.html
I can say that getting a Clover USB bootable disk working with my existing GA-X99-UD4 was almost impossible. I'm not terribly enamored of that motherboard, as it caused me a lot of grief, both from a reliability standpoint, and just lots of annoying idiosyncrasies (like booting to USB external drives, for one, was always a headache and challenging, but there were others, many others) that I just got sick of.
So, I made major progress in getting a Clover USB bootable stick working once I changed my motherboard to a current Asus X99-A/USB 3.1 motherboard.
The key parameter for that motherboard was the following boot line: kext-dev-mode=1 nvda_drv=1 ncpi-=0x2000 debug=0x14e, and of course making sure all the kexts were in the right place in the appropriate directories on the EFI partition of the USB stick I was using. Note that this line did not match my Gigabyte/Chameleon/Extra boot plist. Each motherboard requires slightly different tweaking to work and depending on the motherboard you have, the firmware revision, etc, can make getting all of the parameters to work properly very challenging.
Plus, of course, I have an X99 motherboard with an unsupported kernel and a GTX980 display adapter, unsupported, an audio device ALC1150, also unsupported, especially so on an X99 motherboard, so apparently, I guess I do like a challenge. Yea, maybe......and somedays, maybe not.....
Back to how to migrate (the way I did it): The key is: have a good bootable Clover USB stick
- I took an older used "spare" 350 GB drive I had sitting around and connected it to my system.
- I formatted it to OSX (10.10.5) from my existing working Chameleon/Chimera system drive.
- I then installed Clover 3.3.3.3 on it (the "spare" drive).
- I used EFI mounter v3 to expose the EFI partition on the USB stick, and also did the same on the spare drive.
- I copied the contents of the EFI partition on the USB stick and overwrote the EFI partition on the spare drive
- I then used Clover Configurator to make sure all of the settings on the config.plist on the spare drive were correct.
- I used Carbon Copy Cloner to clone the existing Chameleon/Chimera system drive on my working Chameleon/Chimera drive to the spare drive.
- Once that was done, I moved the Extra folder on the spare drive from the root to the desktop.
- Next, I shut the computer down, went into the bios to make sure that the boot drive was now the reconfigured spare drive (now running Clover). When I booted, I could tell it was correct because, in the boot menu, it showed the drive as UEFI.
- After booting, I made sure that the spare drive was now working properly with Clover and booting correctly, and not using Chameleon/Chimera to boot or load the system.
- I formatted the former working drive, installed Clover on it, exposed the EFI partitions on both drives, copied the EFI contents from the now working spare drive to the newly formatted previous drive.
- Finally I used Carbon Copy Cloner to clone from the now working "spare" drive to the other drive (the one that used to use Chameleon/Chimera to boot and load the system).
- Once done, I rebooted, disconnected the spare drive and booted.
Worked perfectly, at least for me.