Why would anyone go to the expense of replacing the rotor - it's total overkill for MOST LT's since it isn't even CLOSE to being out of specs, and for MOST LT's drivers it will stay that way well over 100,000 miles. My first one was still good at 140K and only on the third set of pads. It just plain doesn't get that much wear and tear since it's only providing 10% of the stopping power.
With the rotor off to the side - and hanging from a piece of bailing wire - sand it on both sides with 200 grit Garnet paper stapled to a wood block - while the wheel is rotating in first gear on the center stand. (make sure someone is sitting on the bike just in case...) Garnet paper is the only type that is hard enough to cut the metal. Do not even think of using any other type of paper since you'll leave residue on the surface of the rotor. You are trying to remove ALL residue to have a spotlessly clean surface.
After sanding wipe down with Acetone.
Inspect the calipers for proper function, then pop on some new pads - I still think BMW's are the best but it doesn't really matter what brand. Bed the new brake pads in properly with 10 progressively harder and faster stops, making SURE not to allow the pads to contact the surface after each stop - in other words once you have stopped release the rear brake immediately. You want to get them HOT.
No more cowbell.