Pulsing brake pedal is the classic warped rotor symptom, and the fact that you just had brake work may point to them. Did the shop machine (turn) or replace your rotors? If they machined them, they may be too thin and, hence, prone to warp. Are the lug bolts torqued to specs? Some shops overtighten lugs and uneven lug torques can actually warp the rotors and cause pedal pulsation. I'm not too keen on the lumpy idle theory -- you feel it in the brake and the idle feels smooth at rest, right?