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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

Oops, sorry.

I always measure to be sure.  Here are three quick ways to verify diode anodes:

If you have a diode test setting on your multimeter, it will read voltage (Vf) when the red (+) lead is on the anode, and no voltage when the red + lead is on the cathode.

If you don't, use the ohms setting on your multimeter, it will read a resistance (1k to 100k) when the red + lead is on the anode, and a much higher resistance (megohms) when the red + lead is on the cathode. 

Connect a battery to an LED thru the diode.  In one direction (anode to +V) the LED will light up, in the other direction (cathode to V+) it won't.

You're right, this doesn't address any issues of clarity, flabbiness, bassiness, etc. I'll leave that to those of you with better ears than mine!  But if you're interested, as an example here are the mods I would suggest to adjust a stock Tube Screamer's filters for drop-A baritone guitar.   You'll only need to replace 4 caps.  I don't have a baritone so I haven't tried it.  If you try it and like the results, I'll add another post (probably TL;DR) to run thru the process I used, hopefully this idea will be useful for other pedal experiments for baritone.

Using the Electrosmash TS schematic and analysis as a reference:  https://www.electrosmash.com/tube-screamer-analysis

(Input and output filters are fine as-is, they're HPF at 16 Hz and <2 Hz respectively.)

• Feedback loop HPF = C3 + R4, move 720 Hz to 498 Hz by changing C3 from 47n to 68n.
• Feedback loop LPF = C4 + R6 + 500k pot, at max gain move 5.6 kHz to 3.6 kHz by changing C4 from 51p to 80p (use a 47p and a 33p in parallel).  LPF effect is reduced as you reduce gain, and C4 value becomes less relevant, the maximum cut is at full gain.
• Main LPF = C5 + R7, move 723 Hz to 482 Hz by changing C5 from 220n to 330n.
• Tone control: For pot clockwise, move 3.2 kHz cutoff to 2.2 kHz by changing C6 from 220n to 330n. The rest of the tone pot range also drops a perfect 5th by changing C6 and C5 to 330n.