Many brake problems can be attributed to installer error.
I advise anyone doing their own brake work to invest in a dial indicator, this is the most important tool for a brake job. Not a power bleeder, piston tool, etc. while all beneficial are not a necessity.
This one is fine for the DIY and will pay dividends many times over.
http://www.tooltopia.com/fowler-72-520-4...id=scsho6812369
A 0-1" micrometer is a good tool have for checking rotor thickness again a cheaper one will work fine. This one is okay.
http://www.amazon.com/Fowler-52-224-001-...+micrometer+0-1
Start by cleaning the hub and back of the rotor where it mates to the hub with a disc, wirewheel, etc.
Use all the lug nuts to secure the rotor using conical washers, tighten them them to spec. Mount the dial indicator.
Check the runout if its more than 0.002" remove the rotor and reposition it and measure again.
Washers..
http://www.brandsport.com/grla-79916.html
If repositioning doesn't correct the runout you need a shim. You can buy them from Napa or RockAuto and other places. Use a full tapered shim not just shim stock in one place.
Using the dial indicator find the high spot and low spot and subtract, this is the shim thickness you need.
Mark the low spot as well as the stud closest to it, remove the rotor and put the shim with its mark pointing to the marked stud.
Put the rotor back, secure it and retest.
Shims
Next check the caliper alignment. This is rare but with reman calipers and reground brackets it happens.
Pump the brakes to close the pads on the rotor.
Using an 0.002" feeler gauge check between the pad face and rotor at the top and bottom of the pad.
If the bottom of the outside pad and the top of the inside pad is more than 0.002" e.g 0.005"
you need to add a shim washer to the bottom caliper bracket between the bracket and knuckle.
Vice versa if it goes the other way using a shim on the top bolt.
You can use shim stock for this job.
If only one pad is out then wither the piston face is off or some rust is preventing proper seating of the pads.
You can usually correct this condition by cleaning or dressing with a file. If its way off and its all clean you probably have a distorted pad backing plate.