Runoff ph is the only ph that matters in terms of diagnosing a plant in my opinion. I'm no expert either, but at 5.6 that plant can't take in anything.
I also have a feeling that there is a reason OP didn't post pics. It's not a "new" thing. He's ph'ing the water and then adding those...
Up to you. Wherever you want to start counting. There's no shame in counting that one from pop, even if it's stunted. It's a mutant. That's cool enough.