I think the basic answer is that the project you started from likely doesn’t work as shown. The original project doesn’t have schematic routed (and I am too lazy to try and route it), but looking at breadboard the op amp negative inputs are both grounded and the positive inputs connect to signals. Without feed back resistors this will act as a comparator not an amplifier. As long as the signal in is higher than ground the output will be the positive supply voltage if the input is less than ground, the output will be ground. You likely need to find a working op amp amplifier circuit (I’d suggest building it to make sure it works) and then make your changes with the digital pot. There are lots of op amp tutorials on the net.
Peter