I doubt that they put new skins on CPO vehicles.

As for your current repair, if it were me I wouldnt have any worries about it. High performance (i.e., speed rated) tires are still serviceable at their rated speed with proper repairs as long as the hole is somewhere between the shoulder treads (which it sounds like yours is). And since its likely that you're not using your Expy as a race truck or police vehicle, you shouldnt have any problems with the repair.

I doubt Ford will give you a new tire (though it never hurts to ask) and I personally wouldnt want two different tires on the same axle, but thats just me.