[Idaho Red Rocket 3]

You should not have a clacking sound at all. Something has to be loose or not set correctly. I changed my 1998 Base to drilled rotors and new pads. They worked great and no funny noises. There are several things that could cause this sound 1 time each time you drive it. It would depend on whether or not you are always going forward or if you back out of the garage or on to the street. I would suggest looking at the following things. The way you describe it sounds like something is loose and it is resetting when you first apply the brakes.

These are just some things to check to eliminate possibilities.
1) Did the rotor set keeper bolts get tightened properly ? If they are loose or broken the rotor could be slipping against the wheel studs. Although you would think the wheel stud bolts torque to 96 foot bounds would hold it anyway.
2) Wheel stud bolts. Are they torqued to 96 foot pounds ? Are they not broken ?
3) Caliper bolts. Torqued to spec ? I don't remember the number.
4) Are the pads the right size for the caliper ?
5) Pad springs seated correctly ?