Hoe bout the Hawk pads? Kinda pricey though. I think they were about $100 for the front set.
You'll need some good brake lines though...there was a recall on the '94-98 cobras because of failed lines when using better pads. I think the 99-later lines are up to snuff.
For what you paid for your calipers...you could buy $160 brake pads and still have only paid what i paid for my calipers alone.
Get some rotors yet? If you stay with factory ford units...get the 99-04 brake rotors. They are made by Brembo and are better quality than the ones made in 94-98.
Hope that you did not paint the other side of the hubs! If you did, remove the paint there so that the rotor fits flush against the hub.
Before installing the rotor on the front hub or rear axle flange, coat the hub/flange with a light coat of anti-seize so you can remove the rotors later without a BFH.
For the street, you can just use the base Aimco pads or what ever you can get like from http://www.discbrakesrus.com
Otherwise, use the Hawk HPS. HEre is a chart from MM on the Hawks: