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The Calipers in The First Kit You Showed are Basically Replacements For the Gt-500 Calipers.
Here is The Ford Kit To Upgrade To Gt-500 Brakes. You Could Piece it Together & Save Some Bucks. The Pdf Would Be Good To Review For Consideration.
You Do Have The Right Wheels!
On a Side Note I Made Up A Kit For This very Same Deal Before Ford Racing Way Back! 19 Years To Be Exact! But Of Course Once They Had it My Pricing Went to Hell!
those look like Brembo knock-offs or maybe remanufactured Brembos
yes they should clear the 18" GT500 wheels -- they are the same brakes that the GT500's had
I am not sure about the upsized rear rotors, I believe they will fit inside 18" wheels but not positive (they were used on the later GT500's that had 19" wheels)
another way to get improved brake pedal feel is braided stainless lines
I believe this is the kit that I used on my 2010 and it worked out great; though the price has gone up a bit since I did it several years ago. I also added the upsized rear rotors, using a bracket available from a guy on e-bay, since this kit does not include the upsized rear rotors
Altough The Op's Problem Ended Up Being a Misrouted Catch Can Setup I Posted a Lot of Brake Booster Related Info Which You Might Gleen Some Idea's From. Also a Very Inexpensive Vacuum Pump From a FORD DIESEL is Listed.