In order to characterize the ADC you have to get rid of both switchers there (the 3.3V and the 1.1V).
Do replace them simply with linear regulators.
Would be great if somebody comes with a new pcb without any switchers, of course..
The ripples produced by the LC based switchers are pretty hard to filter, as they are rather high energetic pulses.
The setup as it is today is good for less demanding educational purposes, for applications with sensitive analog circuitry or with timing sensitive apps it is simply a nogo.