You should be able to use the factory dowel pins in the stock flywheel. I don't see why you would need aftermarket dowel pins for this install job. Looking at the hardware included on the site, it doesn't seem like Exedy provides them either.
To be honest, I've never performed a clutch install on an 11-14 GT. I've installed clutches on tones of New Edge Mustangs, and one 05-09 GT, but never did I need to replace the down pins in the flywheel. I don't see why the 11-14 GT's would be any different here.
Did you have your stock flywheel resurfaced? If so, I'm wondering if the tech pulled the stock dowel pins out to resurface the clutch and misplaced or lost them?
I'll contact some guys here or friends that have particularly installed an Exedy clutch onto a 11-14 GT to double check, but I have a strong feeling these guys are pulling your chain a little here.
Got Excedy to ship me out a set, the tech at ford said the stock pins were not big enough for this clutch, and that they would rattle and one hard launch and you'll be sitting right where you tried to launch.
They were free, so I guess it was a mistake. The instructions on the clutch kit say they coke with new ones.
Should have the pins in tomorrow along with the car that evening. Really excited to break this puppy in a take it to the strip!! What is recommended for break in?