I would like to change the loop filter components, for example changing the capacitor from 82nF to 100nF as I have lots of 100nF caps to hand. Can I do this?
This is not reccommened. The loop filter is sensitive analog circuitry and must be designed as recommened in the datasheet.
If the loop filter is not setup correctly you can introduce jitter on the ADC sampling clock.
To add a bit to Mike's comment, for usage in wider tempearture range applications I'd recommend using C0G (NPO) capacitors for the 82nF and 10nF PLL filter. C0G has better temperature coefficients then common X7R capacitors and the filter won't detune as much at low temperatures.
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