Ahh, thanks for the clues. For anyone looking for this topic, these are the steps I followed, some may possibly be able to be left out.
add “clock-frequency = <400000>;” to overlay section in the fragment with target = <&i2c_AO>;
sudo ./ldto remove i2c-ao
sudo ./ldto merge i2c-ao
and with that, the scope shows 400kHz clock on my connected i2c device when sudo i2cdetect -y 0
So I modified the device tree file in the wiring-tool folder after calling make, I just want to load this modified device tree. Do I still need to do a reset? I want to keep the other settings the same.