Which level fader are you referring to?  The input gain under Pedal Settings?  You should be able to use adjust the Output Level slider in the preset screen of H9 Control to deal with these level differences.

I’m referring to the level fader on the right of the H9Control “Presets” window, above the “Output” button.

I haven’t seen any volume control in the “Settings”.

I need level settings individually for each preset as they have wildly differing output levels which makes them difficult to use in a live situation.

The differences between input and output can easily be seen in the meters under “Input Gain and Level Meters”.