The audio noise is getting louder and happens more frequently recently. I wasn't sure what was causing it but I knew it had something to do with the foot pedal connections that I made.
I was able to isolate the cause through process of elimination. I checked if there is noise if the pedal is out of the circuit and the result that the noise was gone. I then opened up the foot pedal but saw no problems. I then reviewed the connections and it was there where I found the cause.
The foot pedal's 3.5mm audio jack uses the ground and left audio connections to complete a circuit when pressed.
The female connector where my jack is plugged into has a ground connection that is connected to it's body.
Now this shouldn't be a problem when used normally. Turns out I wasn't. I designed the circuit so that the 5V wire goes through the foot pedal. Because of this, the body of the female connector is connected to 5V, and when the wires were bunched together, interference somehow happens.
So what I did was I connected the foot pedal through the ground wire. Which would ground the body of the female connector, which is what it was designed for. I then re-made the circuit and resoldered them so that there are enough spacings between connections.
It seemed to have worked! Now the noise is completely gone.
I am not sure if the switching from 5v to GND fixed it. It may even be the spacing allowance that I made. Or maybe redoing the whole thing fixed any loose connections. Whatever the case I'm glad that it's fixed.