Who has Dr. Diff 8 3/4 rear discs?

Here is how my lines are run, could it be the way the flex is routed?

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Possibly. In the second picture it looks like your might be just as high as the bleeder is. Hard to tell from a picture, but if the line is actually higher than the bleeder you could have an air bubble trapped in there.

Cass would know better than I do but I'm not a fan of the calipers being run without the emergency brake cables. Some rear calipers won't adjust without the parking brake. I don't think the mustang calipers fall into that category, but I wouldn't rule out the cable being unhooked as contributing to the issue either.