Based on Atmasphere's advice, I also tried higher loading, going from 475 ohm to 121 ohm (not so easy on the Io, changing a jumper at the back). Result? Musicality: great. "Echoes" sounds a bit sweeter, more mellow. I realize, I am moved by the music - always a good sign. Is it also a bit duller, rolled off, or contracted? Not sure. Maybe a little. I will have to try the middle setting (243 ohm). Testing with the Hifi news record, I did not find any change in the resonance frequency, it is still down at ca 7.5Hz.Loading should not affect the tonality of the cartridge, as essentially the loading is to prevent a resonance at very high frequencies from occurring by detuning it. If it made for an improvement, it means that the phono section is sensitive to RFI at its input and may have stability problems (but not the sort that cause woofer pumping).
In an ideal situation, the cartridge should be loaded by 47K. With low load resistances (like 100 ohms) the cartridge has to do more work, and that energy coming from the stylus motion means that the cantilever has to be stiffer as well. JCarr and I talked about this at Munich a few years ago.
Now you mentioned that you examined the platter bearing- did you lubricate it? If the platter bearing was dry, the simple act of removing the platter and reinstalling it may have gotten enough lubricant in place to result in the reduced woofer pumping. So the arm and cartridge combo not being ideal might be a complete red herring.