Ok. Here's the small step that I think could have screwed my initial attempt(s)--probably a combined 5 hours of them. (It turns out that I have 16 minutes to happily write this because El Cap is finally installing to my right.)
When you download and run Clover, and you give it the install directory, that's going to be your main drive (probably). You end up with a folder called EFI, in which, presumably, lives your brand-new Clover files. This is key: of course, those files won't reflect any file changes/additions/deletions that you had to carry-out, in order to get your original Yosemite (fresh) installation going.
I think my mistake was thinking that, when copying and pasting the new EFI folder (result of fresh Clover install) over top of my EFI partition's content, and choosing "merge", that all would be well. It wasn't. I'm not going to investigate what a "merge" paste actually does, because I only wish to point-out that this COULD be the cause for trouble and the beginning of a side-trail from you'll need to backtrack. (I think certain files were unintentionally copied over that shouldn't have been, or something like that--although what can you really hope from such a user-friendly file copy operation descriptor.)
The first symptoms I encountered were solved by trying combinations of boot flags. Then I got to a blank white screen that never went anywhere after 40 minutes of waiting (no beach ball on mine, unlike others). So, fine, I said--let's erase this whole damn EFI partition and replace with the brand-new vanilla Clover EFI file. This opened me up to even worse issues--presumably other things that survived the merge operation were now gone.
So that was what I now know was some very destructive troubleshooting. (I had the intact USB drive with the EFI partition as it was when I was first able to boot into the Yosemite installer and subsequent Yosemite instance, so I was able to boot back and forth between working Yosemite and non-working, updated Clover and the subsequent (failing) El Capitan installer.) I decided to revisit how I got OS X on this thing in the first place. I had followed the RampageDev guide, and there were some VERY specific things and files I had had to mess with. Basically--and I know this has gotten long, but I now have 11 minutes remaining on the ElCap install and sometimes an anecdotal troubleshooting description can trigger some lightbulbs in your head--I decided to go the other way around.
Firstly, consult and respect your original guide that you may have used for Yosemite. I had followed a guide that instructed me to choose "Customize" during Clover install, and to choose to install several options under Drivers64UEFI. So, I made sure to do the same thing when updating per this guide (reinstalling, effectively, because the installer just backs-up your existing EFI folder and puts it in EFIbackups or something like that). There were also other files included in a .DMG that I will get to in a second.
Since I had a working copy on USB, I could afford to delete EFI on the EFI partition, and to copy the brand-new Clover EFI folder onto my EFI partition. Revisit how it was that you got your Yosemite instance booting in the first place. Did you paste an SSDT.aml file specific to your hardware like I was originally instructed to do, and then completely throw that out the window upon following this guide (however correctly/incorrectly)? Grab that file, do that again. Consult your original guide. Do those things first, again in your new Clover install (whose file contents, again, are now in your actual EFI partition) Make the config.plst changes in this guide. Copy the Kexts you had before--I put them in every GD folder 10 and up--so including 11, and also "Other".
El Capitan is welcoming me by name ... happy Friday! Now back to Logic, and here's to hoping that the GUI instability issues were related to the OS and that ElCap has some bug resolutions waiting for me ...
