Very interesting observations - I too find the SD card music stunning.
I too came from the BM5000 and CD50 route to the BS4 and BL6000; even having RL 6000s at one stage ... I do not recall having the same sense of disappointment you have.
Just a suggestion, move the BL 6000s to where thet can be driven directly by the BS4 through a pure Powerlink cable connection and see what a difference that makes - just to see if there is anything in the hypothesis that the old cable arrangement is incorrect.
Remember to flick the switch on the BL 6000s from LINE to L and R respectively.