Is it the sub-woofer (not the 8" fullrange) where you see the excess excursion? I presume so, since you call it a "woofer," but thought I should make sure. I am not at all confident I know what you mean by " pumping like crazy on the phone" - what does a telephone have to do with infrasonic disturbances?
You mentioned implementing a high-pass filter at the phono input - is the problem only with phono? If your mention of the phone means you are driving the preamp with a smartphone, I am guessing the problem is on all inputs. In that case, the best place for the filter is between the preamp and the sub amp. If it were mine, I'd put the filter inside the sub amp, since the capacitor value depends on the sub's input impedance. If you put it in the BeePre, it will only work properly with subs that have the same input impedance as the Kinergetics.