I just finished installing as well... here's how it went and my question...
I've got a 1,1 flashed to a 2,1 and I'm running an Apple ATI 5770 video card . I was running Yosemite (with PikeYoseFix) on an SSD.
Took the SSD out my Pro and used a USB adapter to connect it to my MBP. Booted the MBP which is running Yosemite and downloaded El Capitan from the app store. Copied it to the applications folder of the Yosemite install on the SDD. Opened the El Cap installer from that location and let it do its thing... It also took around 30 minutes for me as well, give or take.
1st attempt - I followed the directions posted by RX2904. Thanks for posting your directions, they did eventually work and I don't know what went wrong the first time.
At step 4 of his guide, I accessed Terminal (and followed the guide) from my MBP's Yosemite install, not while booted to the El Capitan install on the SSD connected to the MBP. You type in Terminal defaults write com.apple.finder AppleShowAllFiles YES and then hold the option key and right click on the Finder icon in the dock and click Relaunch
Move along to step 5. You access those locations on the El Capitan install. The two folder/locations that you are looking for are /usr/standalone/i386/ and /System/Library/Coreservices/ which are very easy to view once you've put the command into Terminal to show hidden files/folders. As stated in the guide and by many others here, you must take a few extra seconds and verify that the file sizes in order to make sure you've actually changed/replaced them. Don't be lazy or too sure of yourself...
For the locked boot.efi file - I followed what RX2904 put in his guide and I had no trouble. All I did was highlight the locked boot.efi file and then hit CMD+I and then uncheck/tick the LOCKED box under General.
Now... the first attempt, this is where I stopped following the guide. I didn't try to access the recovery partition and replace that boot.efi located in com.apple.recovery.boot folder of the Recovery partition. Instead I just ejected the El Cap SSD and popped it into my Mac Pro and attempted to boot. I was greeted with a kernel panic and some error message about not being able to find/load drivers for ACHI or something, someone else in this thread has had the same issue. I tried multiple times to reboot and got the same thing each time. So I connected the SSD back to MBP and attempted to copy/inject the Extensions folder from my Yosemite install on the MBP to the El Capitan SSD install and reboot again once I put the SSD back in the Mac Pro. Well, that didn't work either. I still got the same crappy error message. I then tried to repair permissions, verify the disk and all that wonderful jazz that we all know we either should do or should try. Still no luck... So at this point I started to have a kernel panic of my own and was thankful I do regular daily Time Machine backups except I didn't know where my Yosemite installer was that Hennesie was nice enough to share. By the way guys - donate to these guys who accept donations - without them, you'd probably have to pony up way more cash for a new Mac or at least a used one that would run these new OS X versions.
So... freaking out at this point... I decide to just re-install El Cap once more onto the SSD. I don't think you have to do a clean install by formatting the drive you chose to use. In fact, if you don't it makes it easier cause all your stuff will still be there once you get it booted and running again. So I went through all the steps in the guide (again)... at step 6 this time, I let the MBP boot the El Cap install. I did this mostly to just verify that the install did work, which it did and I don't know much about all this except how to duplicate what someone else has already done. I then rebooted my MBP to its Yosemite install, accessed the recovery partition of the El Capitan install and replaced the boot.efi file there as well.
To access the hidden partitions, open Terminal and type
defaults write com.apple.DiskUtility DUDebugMenuEnabled 1 then relaunch disk utility and click on the debug tab and then choose show every partition and then highlight the Recovery HD partition and then click Mount. You'll see it on the desktop and with hidden files still showing, you'll see the folder location to change the 3rd boot.efi file that you need to change.
So, after all this, I put it back into my Mac Pro and surprisingly it booted and worked. I'm not sure exactly what I did wrong the first time, I followed the same directions both times and used the same boot.efi files both times as well.
---------------------
Now, my question... I too want to know if we can use PikeYoseFix to make sure the replaced boot.efi file(s) doesn't get overwritten somehow. I've seen it asked several times throughout this thread and haven't seen anyone answer yet.
Once you get to El Capitan I have no idea how to access hidden partitions cause Disk Utility is totally different and the Terminal command to show it doesn't seem to work in El Capitan... So at this point, I'm considering either going back to Yosemite OR making a partition to install it on and restore a recent TM backup so I can have a somewhat more functional Disk Utility. I've also read that you can't resize partitions with the new Disk Utility like you could before... anything I'm wrong on in this post, please someone correct me so I don't confuse other users. Thanks to RX2904 for the guide. Thanks to everyone else for their input and time, thanks to Pike and Hennesie also and remember guys - Please donate to these guys - especially if you use anything they post/upload.