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It works! Turned out that I did have a clock signal but my arduino doesn't have a fast enough sample rate to measure it.
Instead, transistor Q1 was causing trouble as I had confused the correct pin ordening. Once I had this sorted out, I only had to adjust the bias trim a little and the pedal came to life.
Definetely made some rookie mistakes, but I'm glad it works now and I will make more pedals in the future.
Cheers!

Okay, tried to detect a clock signal using arduino, the signal from my LFO ideed seems to work and is affected by the depth and rate knobs.
Output pins 10 and 11 of the 4047 don't generate a clock signal however. I don't fully understand how the 4047 is supposed to generate these clock signals, as to me it seems that pin4 and pin5 would not be allowed to be connected together.
Obviously I'm wrong, a brief explanation of how the 4047 is used here could really help!

I could ask my university to let me use a scope for a couple of hours. That would only be possible in a couple of weeks however. For now I will check the trim again and double check all connections.
Thanks for all the help so far!

I've done that yesterday, both visually and with a multimeter. I did indeed find two missing connections and fixed them. Then I checked again and also measured all resistor values and checked all capacitors, they all seemed to be correct.

Here are my voltages

IC1 (4558): 3.96, 3.95, 3.86, 0, 7.89, 3.95, 3.95, 3.94
IC2 (MN3007): 7.22, 3.59, 1.28, 0, 0, 3.58, 3.46, 3.46
IC3 (CD4047BE): 7.01, 0.11, 6.64, 7.18, 7.18, 7.18, 0, 0, 0, 3.57, 3.58, 0, 7.01, 7.17
IC4 (LM358): from 1.06 to 2.10, 3.54, 3.51, 0, from 1.28 to 2.66, 1.93, from 0.51 to 6.21, 7.81

I'll also include a pic, but I'm aware that it's a really messy design. It's my first try at etching (and making an actual circuit in general) and had to make it in a rush at my university.

Hi everyone,

I've been trying to build the touchstone modulation effect from etcher's paradise, but I'm only hearing the original clean signal comming through. I've also noticed that none of my potmeters seem to do anything.
Could this be the result of having a broken MN3007? Apparantly it's pretty common for MN3007's to not work. I'm using one from XviveAudio, which to me seems a quite trustworthy brand.

Any feedback is welcome!