Well, it seems that I had missed out on soldering the input jack to the stomp switch and the circuit was barely connected except by gravity. This might have explained the squealing noise that was present prior to inserting a capacitor to ground next to the initial pull down resistor. I'm not sure if this effectively created an R-C filter that took out the high pitch sound.
Anyways, there are some problems with that build which I need to modify, the filters didn't work as I had expected them to. The stock Low pass filter's sweep was only about 1/2 of the potentiometer. I would have expected it to be the same as the rat, but for some reason it doesn't. I think it could have turned out differently if I would have used a Linear instead of Logarithmic taper.
I still want to use the enclosure, but with something that different. I have a Big Muff PCB and I'm going to try out some updates/modifications and hopefully that goes well. I'll try to do a better job documenting what I'm doing.
My schedule is pretty busy, but slowly I'm starting to think about the multi-effects time based rack unit. I've got a Madbean Delay PCB...