I no longer have any idea of what you are attempting to do.
OGNerd, Sorry for the confusion. I am a doctor, and I can talk all day in a language many would not understand, so please understand that I do not yet understand some of what is said in this chat. But I am working to understand, and I admire those of you who speak Mac Pro. I have been following this thread for weeks now, but I waited until this past weekend to attempt an upgrade, when Pike posted his "final" version of the boot.efi. What I have done so far is this:
1) There is a Mac Pro 4,1 at my office. I used this machine and DiskMaker to create a bootable OS X El Capitan USB installer. I tested it on that machine and it worked. I then used this USB installer to install OS X El Capitan into my Applications folder and onto my desktop.
2) I used the Macrosxbootloader by Pike R Alpha to download the latest version of boot.efi onto my desktop.
3) I replaced the boot.efi in my computer in the CoreServices, i386 and Recovery files. I was having a problem previously unlocking and replacing the boot.efi in the Recovery disk, thus a previous post, but I was able to resolve that thanks to all of your help. My last post shows a picture of all three locations with the correct boot.efi file in place, just in case there was a question.
4) I then used the OS X El Capitan installer that was on my desktop to attempt to download El Capitan onto my computer. When the computer rebooted, it was into the OS X Disk Utilities screen. I tried to Reinstall OS X from that screen, but it chose Yosemite rather than El Capitan. A second reboot resulted in the same situation.
5) I used a second drive on my computer with Carbon Copy Cloner to boot back into Yosemite.
6) That is where I am currently stuck.
Tonight I will try the things Pike R. Alpha (thank you for the honor of your direct response) suggested.
Steve