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That will be my belated birthday present to myself.

What value is your C9?  It should be 390pF, but it's the same size as your 390nF C5.  If you have a 390nF in C9 you're letting way too much signal bypass the negative feedback loop resistance, which would kill all of your gain.

And the winner is... OMG, do you know how many times I've gone through these... I seriously need to buy you a beer!
Well done. 

I'm happy you're happy, but I wish that would have actually fixed your problem.

Swapped the errant cap and nothing.  Swapped the IC's and got gain finally  but glitchy when I'd dig in a little. Then it just started sputtering.  Gonna put it away now before someone gets hurt.

I take it you switched to a quad op amp with a higher voltage rating?

What value is your C9?  It should be 390pF, but it's the same size as your 390nF C5.  If you have a 390nF in C9 you're letting way too much signal bypass the negative feedback loop resistance, which would kill all of your gain.

R29 feeds to R2 which feeds into IC1 pin3. Looks like R29 end @ IC3 pin8 is not soldered.

R29 does look dodgy, but it also feeds every point in the circuit that is receiving ~4.5V (VB).

**EDIT: I checked R7 coming off Pin 7 of IC1, and I've got a 430k instead of 422k. I couldn't find any 422k resistors but still had 430ks, so I used that instead. Is that enough of a difference to cause the problem? Back to checking...

Yeah, there may be a few dodgy solder joints from what I can make out in those photos.  R13 stands out from here.

But what are the color bands on your R7.  A Four-band 430K resistor should be yellow-orange-yellow-gold.  That third band looks like it might be brown for 430R instead of K.

That would explain the gain pot issue, but it wouldn't explain the weird voltage on IC1 pin3.  i would suggest reflowing the solder on that pin.  Can't tell if it's bad, but it's one of the few things that could explain an out-of-place voltage.  I checked all the resistors in that part of the circuit and they looked good.

Edit: Oh, and to answer your question, no a 430K in that R7 position (assuming that's what you really have) wouldn't matter a hill of beans compared to the specified 422k.  Those odd values in Klone circuits come from component measurements, not necessarily their spec, so the original value was probably 420K or 430K and the part was somewhere within the range of its 5% tolerance.

Okay, finally had a chance to test my values. I triple-checked my solder points, everything's clean. Still getting signal through it, but there's still the *very* slight decrease in volume when I turn up the gain knob.

...

IC1:
1=4.67
2=4.67
3=1.19
4=0.00
5=4.64
6=4.67
7=4.67
8=9.24

Actually, I think IC1 pin 3 looks low.  I would expect something closer to the values on pins 2 & 3.  I'm not sure if that would cause the problem you're having, but it's worth looking at. 

Photos!

Q1 : 8.78, 3.92, 3.53
Q2 : 8.78, 3.92, 3.53

Good.

I get 0 for ground at the stomp breakout, but at the pcb it is 0.1mV.

Hmmm.  Touch up that joint on the 3PDT breakout.  Maybe switch out that wire if that doesn't help.

I've verified that all the values are correct.  I swapped the 550s for a pair from a different supplier.  I swapped the 4558 for a different one.  I swapped out the red LEDs for yellow.  I re-flowed all the joints.  No change 

Do you still have the low voltage on the base of Q1?  That's where the most obvious problem was.

One things that's interesting... my strobostomp is plugged in in front of the greenbean, when the GB is bypassed, the tuner works fine.  When I turn on the GB the tuner stops tuning, it still has power, but the strobe LEDs stop moving.  I don't have any clue what that means, but it's interesting?

That is a weird one, and it's probably a good clue once one of us figures out what it means.  But I'd concentrate on the simpler issue (i.e. the transistor voltage) first.  You know that no signal is getting through Q1 until that is corrected.  Also, the joints on your Fat switch look pretty bad.  Touch them up and add solder.

--

Added:  Hmmm.  I wonder if your C1 is bad and you're leaking DC onto your input.

Added later: I'm also disturbed by the fact that you don't seem to have 0V on ground.  That's worth looking into, too.

Are you using PCB-mount pots or solder lug pots?  If solder lug I'd suggest maybe you miswired them, but if you're using PCB-mount pots that's highly unlikely.

I'm guessing it's an incorrect component value, but it could be a bad solder joint or even a short.  Post some good photos of both sides of your board so we can check those out.

And, unless you know all your voltages are right, go ahead and put up your IC pin voltages, too.  Good luck!

Congratulations on making one of the best and most thorough Tech Help posts I have ever seen.  Future Tech Help posters should use this as a template.

The base of your Q1 transistor looks low.  I recommend measuring the voltage on either side of R3.  You may need to reflow the joints on R3 and Q1's base.  All other voltages look totally believable.  Good luck!

I do wonder what the hell is up with the pots and pans sitting on the sound engineer's desk.

Merlin Blencowe's U-Boat is available as an etch from his own instructions or as a fabbed PCB from TH Customs.

Cool.  Glad you got it sorted out.

If the LED doesn't light up and you don't get bypassed or effected signal, you've either got a power issue at or around Q1 and R32 (as you've guessed) or you've miswired your switch.  (I'm assuming you've wired this up for buffered bypass.)  If you're 100% sure your switch works correctly, then check out the power.

Do you have 9V after Q1 or on R32?  If not, you can jumper Q1 drain-to-source, either with a wire or a 1n5817 diode.  That MOSFET is just there for polarity protection.

Mac Walker makes a wedge enclosure he sells over on DIYstompboxes.com, but it's slightly larger than a 125B for all dimensions.

I've never seen a manufactured sloped enclosure smaller than that, but there is a thread around here somewhere where someone chopped a 125B down into a wedge shape.  I suppose you could do it with a 1590B, but at a certain point you're running out of room for your 3PDT lugs.