I wouldn’t worry about your Rega alignment - Roy Gandy doesn’t believe in such nonsense 😉 as long as the 3 cartridge mount screws are in place & your Elys 2 is tracking @ 1.75 grams. The anti-skating slider behind the tonearm rest can be set slightly under 1.75 for optimal results if the turntable is level.
I would though, try listening for minute differences in tracking force +/- .02 grams to see if it has a preference over the recommended 1.75 grams. Tracking force is like a one-knob tone control where you tweak for optimal tonal balance. Too high VTF equates to bass heavy & vice versa.
With the Musical Surroundings phono, the pair of 4 dip switches are only for gain or volume. The pair of 8 dip switches are for loading.
Since the Elys 2 has a lot of output, 40 dB (all 4 off) will most likely be your best setting. The next level to add volume is 44dB (only 4 of 4 on).
From memory, only position 1 of 8 (capacitance of 200/300 or 100/200 pF) and 8 of 8 (resistance of 47/100 kOhms) is relevant to your Elys 2.
More capacitance and less resistance will soften the tone & vice versa. FWIW, realize that 47kOhms is the Elys 2 standard for positions 8. Positions 2 ~7 off.
That’s all you’ve got. Hope this helps!