Q: Brakes are pulsating

One day I was driving and noticed I wasn't rolling back even on 5-7 degree hills and the car seemed slower. Shortly after, my brake pedal started pulsating. I checked all of my brakes and found that rear passenger caliper was seized. I had a new spare and put it on along with new rotor and pads. I also replaced the pads and rotor on the rear driver. Upon test driving I found the car rolled back and was normal, but the brake pulsating was still there. I used my dial indicator and measured the lateral run out on all of the rotors including the new ones. The worst rotor was 1.8 thousandths. I also measured the thickness of all four corners of every pad front and rear to see if there was any uneven wear. Biggest difference was around 0.3 mm. I also adjusted my parking brakes. I made sure all the brackets and backplates were secure and all hardware/pins were lubed up. After the car sits overnight, the pulsating goes away and returns shortly after some mild-moderate braking.

My car has 140000 miles.
My car has a manual transmission.