I think you've done the right things, the fuel supply was a big one that may be okay now. The E85 takes a lot more flow, more fuel for the same A/F at an rpm, so selecting the proper pump/FPR/lines is less common knowledge to figure out. The TPS is hard to know if that had an affect on the tune in it now, when it was made etc.
Most people with EECIV like the quarter horse a lot, they love it for ease of tune. I don't know how easy it is to learn it, but I think it's not a big deal. I know a member on the Corral who has done several Mustangs he owns, plus his sons, friends etc. He has more vehicles he has posted about than I can keep up with. I'd ask him if I was working with EECIV etc, his name is David Caflin, he's in FL, and on the SBFtech forum. He's got 302's and 306's with massive intakes and TB's, running smooth at all rpm's etc. He likes big heads, intakes, TB's on any SBF, I don't think he's done any boosted tuning, but he makes the stuff he does seem easy. I think I'd try to ask him or someone similar who knows the quarter horse well like that. They'd more quickly run through the possibilities of the symptoms you've had.