It seems like it’s all working correctly as you described. Is the pedal not sounding correct to you?
Remember the calibration values given in the manual are arbitrary values to just ensure the circuit is working more or less correctly, and by your measurements, it is. Keep the high trim pot set to whatever gives you the lowest value and then adjust the low trim pot until you like way it sounds. Make up for any low signal levels with the gain trim pot.
Also remember when you measure the resistance of the test points, you are measuring the LDR resistance in the optoccoupler while the LED light is shining on it, which the trim pot is controlling the brightness of (see the schematic). That is why the resistance is going up to megaohms/open when the light/power is off.
-Brach