I'm going to circle back around to my first post (#2 in the thread). If you can take the internal drive and put it in an external USB case, and all is well like you just described, then you have a bad internal drive cable. So you need to replace the cable then put your original internal drive back inside and all will be well.
https://www.ifixit.com Sells the cables.
Weaselboy, boy am I glad to see you finally!
Let me also repeat what I said, since I know this thread is getting hard to follow! I responded to your post this mornng with... (Part of Post #23)
Next, I tried the same thing with my production/latest HDD. That is, I mounted the latest HDD into my case - with no other HDDs attached - and booted up using Option, and unfortunately I was stcuk on the grey apple screen again.
That says to me that something is dreadfully wrong with this MBP, and it probably screwed up my production HDD.
As mentioned in Post #24, I have to go buy a USB hub and a 3rd external enclosure later tonight since I can't use any HDDs internally.
Questions:
1.) What are the chances that my original HDD is toast?? (My internal HDD is only maybe 3 months old.)
2.) Once I get a USB hub and 3rd enclosure working, what is the smartest next move to make?
Should I try to use CCC to clone the main HDD to my blank HDD?
3.) I read yesterday that if you reinstall El Capitan it could fix any issues with the EFI partition and that it will NOT erase my personal data. Is that true??