That sounds like you need to re-assign the conflicting connections, which you figured out yourself. However, A4 is one of the I2C pins, which the RTC uses to communicate with the microcontroller.
If I’m understanding you, you want the datalogger + clock together. I would wire it like this (making sure you change the code to reflect the changes):
D10_(PWM)________SENSOR ARRAY CS
D11_(PWM)________SENSOR ARRAY Din
D12______________SENSOR ARRAY Dout
D13______________SENSOR ARRAY CLK
A0_______________DIGITISER SW1 (can use any pin)
A1_______________DIGITISER POT (needs analog pin)
A2_______________SENSOR ARRAY MIC (needs analog pin)
A3_______________SENSOR ARRAY LDR (needs analog pin)
A4_(I2C)_________MOTHERBOARD RTC (Internally connected)
A5_(I2C)_________MOTHERBOARD RTC (Internally connected)
Note that I removed SW2 as it isn’t used in any of the sketches. You could add it back in by connecting it to one of the free digital pins like D7. If you want to add the RGB Matrix later, use 7, 8 and 9. But, you would have to sacrifice one switch or some functionality to achieve this.
You are troubleshooting well, you just need to know what each of the pins does. That will come with time and experience. Keep it up!