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Ok. . . I think I figured it out. . . . Basically, I'm an idiot. hahaha

I removed the parts for the REGULAR PCB for true bypass operation (R3, R4, C3, R28, R29, R30), and they did not correspond with the same parts for the single sided board. I don't know what I was thinking, or why I didn't realize it before. lol. I'm relatively sure I fried some stuff, so I'm just going to start over and build it all again. Thanks for all the help and advice everyone! I appreciate it.

The first thing I notice is that you're not using the correct charge pump. With the LT1054 pump you need to remove pin 1 of the IC. Did you do that?

Jacob

Hi Jacob!
   Hmmm. . . Well, I just removed pin and nothing changed. It is pretty much the same voltage across the board still.

Your power supply voltages look good on both of your TL072s (IC1 & IC2), but your VB voltage divider (R25 & R26) doesn't appear to be halving the voltage correctly.  You should be getting approximately half of your 9V input voltage at that junction, on the positive lead of C22 and on pins 1, 2, 3, 5, 6 and 7 of your TL072 ICs, but it looks like you're getting the full input voltage in those locations.

Check for a short/bridge around that area and make sure that R26 is making a good connection to ground. 

Got it. . . I understand what you're saying in theory, but the parts list for the single sided version has different values than the normal madbean board. Are you talking about the 27k resistors?

Hi madbean forumites!
    I've been a long time reader here on the forum, but this is my first post. Hopefully y'all can help me out.

I etched and populated a single sided Sunking V.3 board, wired it up for true bypass, and I'm getting squealing that gets louder as the gain knob is turned CCW and lower as it is turned CW. It eventually cuts completely in the fully clock-wise position. The tone is very distorted and sometimes goes into oscillation, and actually sounds kind of like a Fuzz Factory. I pulled out my DMM and here are the voltages. I can't make heads nor tails of the readings. lol. The charge pump I used is a LT1054CP. Thanks in advance guys!

IC1 (TL072CP)
1.) 9.24   
2.) 9.24   
3.) 6.32   
4.) 0.00
5.) 9.23 
6.)9.15
7.) 8.82
8.) 9.27

IC2 (TL072CP)
1.) 9.4
2.) 9.26
3.) 9.24
4.) -8.83
5.) 9.24
6.) 9.25
7.) 9.11
8.) 16.76

IC3 (LT1054CP)
1.) 9.27
2.) 4.93
3.) 0
4.) 4.1
5.) 8.85
6.) 2.54
7.) 1.36
8.) 9.27