I wonder if Evapo-Rust would have been a better alternative to the vinegar in this case? Although expensive, I've had excellent results with E-R in the past even with heavily rusted metal, and it wont dissolve the zinc like vinegar will.
Another thought is that POR-15 will adhere better to lightly rusted metal. I'm wondering if the POR-15 prep was supposed to flash rust the surface by design to enhance adhesion? A side note, in my experience with the regular POR-15 coating, I have never used the metal prep and have had excellent results with the encapsulation, even leaving treated metal out side for years, with no further rust occurring. It was interesting to note that when I would grind off a section of the POR-15, the rust that I had left on was still there, but it was dry and lighter colored, again, encapsulated and stopped by design, not converted.
I'm assuming all of these processes work towards one goal, to stop the rust flakes from getting into the fuel system, and that we are just looking at different methods to that point, one not necessarily being better or worse than the other. It will be interesting to see how long the Red Kote will take to dry and if these "strings" form to get into the system. I'm hoping this works out and that we are just over-thinking the solution.