Thank you again for the inputs you provided and thank you James for the de-soldering technique (I will need it).
Results of further investigations based on your inputs. Stock firmware loaded in Raduino.
I checked also the 3.3V supply of the Arduino and found 3.62V. Stable even when changing menu items and tuning in frequency.
I placed an FT-817 in USB mode with it's rubber antenna near the Raduino (in place in the uBitx). Signals were around S8-S9.
1. Arduino 16Mhz crystal: Measured as oscillating on 15,995.27KHz. Tone would shift slightly and of a similar amount to the Rx audio when tuning the encoder and selecting menu items (see attached recording).
2. BFO was found on 11,996.70KHz which is consistent with the calibration value of 11,996.8KHz. No shift or noise present in the signal received.
3. First oscillator found at 52,090.72KHz for an Rx frequency of 7,100.00KHz. Again no shift or noise present in the signal received when changing the menu items. Change of Rx frequency by turning the encoder would result in a stepped but clean change in tone as received in the FT-817.
4. Second oscillator found at 32,993.95KHz as uBitx was in LSB mode. Clean, stable signal.
So the only clock that resembles the tuning noise but not the multiple tones of the Rx signal is the 16MHz Arduino clock.
I tried to wrap a ground connected shield around the Arduino (from the "top"), but did not find any difference in tones apart from a slight shift as when I place my finger near the Arduino's crystal.
So as proposed above I have ordered a new Arduino and will attempt its replacement on the Raduino.
Attached is the Rx of the 16Mhz Arduino clock.