He built his own highpass filters, so the dip switches probably don't apply. Still, the first thing I always start with is checking with a voltmeter and 1kHz/100Hz tones that the frequency response of the highpass filters is correct.
Then check that the subwoofers are working by checking with the Vandertones and an SPL meter (sounds like you've done that). I have problems with the bass level pots on my Quatros, and I sometimes have to wiggle them a bit if the bass response droops or drops out.
Calibrating the bass response can have a large effect on the midrange transparency, so you may want to redo this (sounds like you may have already). Richard has a newer procedure for this which is a bit easier than the old procedure (it's in the newer manuals online and on youtube).
https://www.youtube.com/watch?v=7C60LoHGtI0
Then check that the subwoofers are working by checking with the Vandertones and an SPL meter (sounds like you've done that). I have problems with the bass level pots on my Quatros, and I sometimes have to wiggle them a bit if the bass response droops or drops out.
Calibrating the bass response can have a large effect on the midrange transparency, so you may want to redo this (sounds like you may have already). Richard has a newer procedure for this which is a bit easier than the old procedure (it's in the newer manuals online and on youtube).
https://www.youtube.com/watch?v=7C60LoHGtI0