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fixed it, to get the calibration running I had to change:
sound = analogRead(receivePin);
      if (sound > 20)

to:

sound = analogRead(receivePin);
      if (sound > 5)

I just disconnected the middle IC to go from 3x to 2xPT2399 to try the calibration,
my breadboard has a fv-1 reverb on the repeats and a mixer to blend them,
I couldn't find the deathklaw schematic to compare but it looks similar from the image in your docs

the receive pin is A0 and that must be working because it calibrates a single pt2399 just fine

no worries mate, 2x pt2399 also fails to calibrate for me,
same as before it seems to start then just ends in about 2 seconds

Tried calibrating a 50k digipot with 1 pt2399,
Then uploaded main code and connected to 3x pt2399,
The delay knob works but it's ignoring the min/max set delay,
Led is flashing maybe 3x fast,
Tap button is way off, and preset and subdiv dont respond,
Was worth a try

Top notch and super designed! Great marriage of through hole and smd, and great looks and finish to boot!
Score!
Edit: Which pcb manufacturer did you use? Cheers!

Thanks mate! I used jlcpcb for the pcb
Enclosure is UV printed by tayda

I put this together using Kicad, found it easier to use than Eagle,
you have to cut the 3pdt order switcher daughterboard off the main board,
0805 resistors, fits in a 1590bb

https://www.dropbox.com/sh/5ixdwblsvl59ap9/AACqANHJG9mEsV7grZMmsqnba?dl=0

Using a 50k digipot,
Disconnected from delay,
Resistance between pins 5-6 and 7 is 30k,
I upload code,
Red led comes on, resistance drops to 1k,
Then back to 30k, green led comes on, this all happens in about 2 seconds

yes 3x pt2399 works with a normal pot,
im wired up same as the v1.2 pdf minus the mod switch,
(also get the same behaviour if I connect the mod switch)

this is what I get when trying to calibrate 3x pt2399
sounds like I hit the jackpot!
serial output and schematic attached

Also currently can't calibrate a single pt2399, I get the first beeps at different tempos with their repeats, then red light goes off and I get clicks, then endless flashing red led on the nano

edit, this started working when I left the usb cable plugged in

I'm trying to calibrate 3x PT2399 for a few days now, I get a beep, then some clicks, then the nano leds flash, but a few hours later it's still doing the same, also the tempo of the click repeats never changes, any ideas?

my RGB led has a different pin out, left to right GR-B is yours and BG-R is mine
so I changed this to fix it
float colorarray[] = {0, LOW, 255, 255, LOW, 0, 0, HIGH, LOW, 0, HIGH, 200};

Mix and Clock B10k
The rest B100k

Nicely done.  How do you get the square cutout so neat?

Stay away from the edge until the last minute
Images are in the build docs showing how I did that