It depends...PBR is a brand that makes both the cobra and 99+v6/GT caliper.
For the 99+ v6/gt PBR caliper you will need to grind on the spindle a little to get them to clear. Not much, I got the needed clearance on mine with a dremel. The threads of the banjo bolts are not the same as the stock 94-95 gt's...these are a killer as Ford stopped making them but they have a cross over part that works but is like 40$ at dealer cost. I know this as I had to buy new banjo bolts and did not believe the parts guy...I get dealer cost threw my father-in-law, the parts guy swung the computer around and said..."WOW they are proud of this".
The lines connected to the caliper are not the same as the stock 94-95 gt either. They fit in a different way/angle.
Youll be glad you did the upgrade, well worth the little amount of work needed. As far as the banjo bolts, I found them on ebay for really cheap from a guy called parts_plus_more who sells them specifically for these upgrades.
The banjo bolt is the bolt that holds the rubber break like to the caliper. It is a bolt that has a hole running down the middle of it. This is how the break fluid moves from the break line to the caliper.
Sell those GT PBR calipers and buy a cobra calipers. the banjo bolts you will need is fine thread M10x1.0 for 94-03 cobra calipers and M10x1.4 for 03-up coarse thread.
The 13in rotor is why the cobra kit is better. You get more leverage with the larger dia. rotor. More leverage = more stopping power.
You will not find someone who will state the the 99+v6/GT stock calipers are = to the cobra.
You will find them saying for the money it is a nice step up from the stock 94-95 calipers. Put a good set of pads on there and it is a nice upgrade from stock.
IMHO for the 100$ I have in mine (without pads) it is a nice improvement. If I go bigger I think I will look into the 4piston SSBC caliper...but that would be a LOT more $$$$.
If you still have the calipers off the car either clean and paint/powdercoat or polish them.
I cleaned the snot out of mine (wire wheel, break cleaner, de-greaser) and painted mine with several coates of that brake caliper paint you can buy. I left the cross bar black and the caliper is red. They look really good cleaned up.