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In your photo, there's not much solder on the north leg of R2, and the same with a lot of the other components.  I think I'd reflow each of your solder joints and add a bit more solder, there should be a small fillet around the legs of each component and many of them don't have that (R8, R5 jumper, etc), which could indicate cold joints = no connection.

Horizontal lugs, with #1 at the top left corner.  The tip-off is the LED, the cathode side must be grounded when the effect is active, so the swing contacts work north-south and not east-west.

I have a bunch of different amps, but the one I was checking on is the Fender Mustang III. I couldn't find anything about input voltage in the manual.

The Mustang III has clipper diodes in the preamp section that will limit inputs above 1.1V RMS or so (3.2V p-p.)

I'd remove the AC input, transformer, bridge and regulator, and replace all that with a +9V DC input and a Traco TEC 2-0921 DC/DC converter.

At Q1-Q4, signal goes into the gate, and should come out the drain amplified. If you have signal at the gate and not the drain, the FET is the location of the problem, if not the source of the problem.

Some things I would check: What parts am I using for Q1-Q4?  Are they known good FETs or could one or more be faulty?   Do the pinouts match the PCB (D-G-S)? 

Welcome back!  I just hit the front page to log in, and it showed me already logged in as dan schumaker, who I'm not.  But after navigating a few pages, my login name shows correctly in the banner, and it's my account settings.

I've got a switch pop I'd like to get rid of and the 1m on the input didn't affect it at all. If anyone has an idea I'm all ears.

Here's a thorough look at popping, very likely one or more of these causes:  https://www.muzique.com/lab/pop.htm

Boy, nearly identical is right!  Here are the two schematics (PedalPCB versions) for comparison.  Mach 1 = Lightspeed, Southern Belle = Southland.  I agree that you might want to differentiate the two sides a bit more, unless you're going for the King of Tone sound with two nearly identical sides.

The only differences are the Gain pot value (500k vs 1M), addition of the two BAT41 hard clip diodes, 2nd op amp feedback resistor (4.7k vs 22k) and the volume pot value (100k vs 250k).  Southern Belle would have a little more gain than Lightspeed in the first op amp (higher value pot) then the added clipping from those BAT 41's, then additional gain in the 2nd op amp.  Volume pot difference is just a matter of where you'd set the knob to get the same level.

What the BAT41 diodes do is limit the input level to the 2nd op amp, their Vf is about like a Ge diode, 0.37 V at 1 mA in each direction (0.74V peak to peak.)  There will be plenty of voltage for these diodes to clip as you turn up the Gain pot, but it's a little odd to do symmetrical clipping after the first op amp generates an asymmetrical waveform (3 diodes in one direction, two in the other.)  The BAT41s will tend to make the waveform of the Belle more symmetrical, the more you turn up the Gain pot. 

Welcome to the forum!

If you'll post a photo or schematic of the existing bypass foot switch, someone here can probably answer your question about it.

In the mean time, it's PROBABLY wired like one of these 3PDTs in the diagram below.  If so, you can add a momentary DPDT along with it as shown.  When the main 3PDT is in "bypass" the momentary DPDT will activate the circuit as long as you hold it down.   When the 3PDT is in "active" mode, the momentary switch has no function.  You can get an appropriate momentary DPDT at Small Bear and other places as well:  https://smallbear-electronics.mybigcommerce.com/dpdt-sf12020-m-momentary/

[Edit: on the momentary switch, the lower set of contacts are the ones that are normally closed (2-3 and 5-6.)  When you activate the switch, the upper set of contacts will be made momentarily (1-2 and 4-5.)

No issue at all, just a tiny reduction in input impedance that you won't notice.

OP07 replaced the LM308 in several Rat models, but they're also obsolete.  You may be able to find either a 308 or an OP07 in SMD and use an adapter board to fit your DIP layout.  UTSource sells used DIP LM308, and if you buy them from the UTsource store and not one of their 3rd party vendors, sometimes they guarantee authenticity.  They also carry OP07. 

Exactly!

This should do it.

It's the same configuration (resistor + cap to ground) as a Tubescreamer, although the values and stock corner frequency are different.  You could use any TS Fat Mod scheme, and substitute the R & C values, if you want a two or three way switchable bass cut.  Instead of adding bass like the Fat mod, you'd be reducing it, but still by switching or paralleling caps.

You're looking for the decade counter (CD4017), not the flip-flop (CD40174, CD40175, etc).  In Mouser, the TI CD4017BE is equivalent to the Small Bear through-hole part. 
https://www.mouser.com/ProductDetail/Texas-Instruments/CD4017BE?qs=IF4wzcbwb3rdXSZhHlgcJw%3D%3D