The build instructions probably ought to call special attention to putting the Atlas Scientific sensor circuit modules in I2C mode (see EZO pH Circuit datasheet pages 40-41 , and EZO EC Circuit datasheet pages 40-41).
As @Spaghet discovered last night (see our forum discussion), the Atlas Scientific EZO pH circuit module can talk either I2C or TTL serial on its TX/RX pins, but TTL serial is the default. You have to do a manual configuration step to put the module into I2C mode. The EC module works the same way.
At minimum, having TTL serial on the I2C bus will interfere with I2C communication, but it seems like overloading IO pins and causing hardware damage might also be possible. I’m not an EE, but it seems like it would be bad for the the pH module’s TX pin in TTL serial mode to drive the Arduino’s SDA pin up to VCC while the Arduino’s I2C master was trying to pull SDA down to GND.
The amplifier will reduce the effects of electrical noise on the high impedance pH measurement. Examples of sources of electrical noise include circulating best pumps, motors, and ballasts for grow lights.