Ok, so, I apologize for being such a pain in the ass, but I managed to get all the voltages. I know that
I was so into many different pcb, that I printed this in horizontal reverse, so I had to CAREFULLY invert all the pins on the ICs and double check every component.

You have.. You did.. WHOAAAAA!!! ... OK, it took a while, but my heartbeat is back and eye-ball's diameter goes back to normal

But now I definitely MUST see it!!

Don't worry: I'm pretty sure the pins match the scheme.
Well if you have flipped legs of all ICs to back without breaking them and the IC's top (side with labels) is now bottom, it should be OK. But you must rotate transistors as well plus pot's will have reversed function (if directly soldered to the PCB from the top).
The cause for the smoke was an incorrect position of the DC lug on the Voltage Supply.
Well, I'm trying to find out what impact could this event have for the circuit itself which I still don't have enough info for ("an incorrect position of the DC lug on the Voltage Supply" could mean lot of things, I need to know what happened "electrically" - shortcut on DC jack, reversed polarity on EM3007's DC pins..), but we can forget about it for now.
It runs at 9V (8.97 to be precise, but come on)
Feel free to be precise (at least two valid digits with proper rounding applied, e.g. 9.0V here).
Here's the list.
OK, where to start.. First, IC pin numbering goes in anti-clockwise circle, e.g.:

So all your right-side IC pin numbers have to be flipped vertically. But OK, I'm able to decode, just for the next time (and maybe to clear some of you confusion if you have tried to map between schemo and layouts)..
Second, at some point you did flip Q1 pins C and E (C is at VCC so it must be like 8.7V, 3.9V is good value for E).
Third, I see that I was wrong with my theory that you are interchanging RT1 and RT2. Long story short adjust RT2 to get
VBias = 5.2V (measure V
Bias at IC1 pin 7 - normally you should measure it at pin 3 of IC2 but you have some mess there). 5.2V is proper bias for MN3007 at VCC = 9V according to datasheet where it must work somehow, you may fine-tune it later. As you have V
Bias (and V
ref) so low now, that's not surprise that you have distortion there (at 1.7V there's not much of swing and used op-amps may not act linear in this area as well).
Fourth, many of your measured values are very hard to believe. E.g. IC6 pin 6 at 0V when directly connected pins 9 and 11 are at 6V, IC1 pin 7 at 1.7V when directly connected IC2 pin 3 is at 0.19V (and there must be connection here because we have heard flanging), 8.2V at RT3 pins 2&3 when directly connected pins 5, 6 and 8 of IC4 have 8.7V, 2.8V at IC6 pin 8 (should be ground) etc. Even some of it may be the real problem, most probably you did just make errors when getting voltages..
Setup V
Bias to those 5.2V and take new measurements at IC2, RT3, Q2 (identify E and C legs yet by some other connected part).
Do new set of measurements at IC3 as well, there must be huge swing on pin 7 (rectangles, you must wait a while as you have probably slowest rate set, it's period should be around 6 seconds) and fluent up/down at pin 8 (triangles). For all pins with swing post lowest and highest value.
Better if I host a pdf somewhere next time.
Whatever.
I swear I don't know why RT1 is going like this: it seems like it's in short. I fixed the eventual joints there, but it hasn't changed.
There should be no DC voltage after C8 and C10, so values at RT1 pins seems correct.
Oh, and I almost forgot: the LED bypass doesn't even work. I soldered it right, following the classic True Bypass Scheme, but it doesn't lights up.
Is this first pedal you are building?
T.