Brake noise

After i did my rear disc conversion, i was getting some weird pop noise from the front left wheel. The brakes aren't mushy and are very responsive. The popping then went away and hasn't came back, but now there is popping in the rear brakes. This only happens when i brake, especially when you lightly push on the pedal and gradually increase the force(happens more often when lightly braking). The popping sound alters from side to side. The sound is hard to describe, but sounds some thing similar to a rock hitting the under body, but the sound isn't as loud, its more of a low pitch sound. I am going to bleed the brakes again to see if it was air in the system, but i just wanted to see if anyone experienced this before.

P.S I torqued all the nuts and bolts to Honda spec, so nothing is lose, but i will check when i bleed the brakes.