Hi Tom,
I spend Sunday at Doug's and we were thinking about your issue. There were a couple of noticeable woofer excursions but I believe each could be attributed to vinyl anomalies. I think from your description your woofer pumping is much more frequent.
There are obvious differences between speakers. Driver suspension, crossovers, internal box pressures, etc. The Salks may simply be use drivers with different mechanical properties and parameters. The fact that your friend also has Salk's and they pump as well is telling us something. I do remember my 10t being susceptible to woofer pumping with vinyl. A local brick and mortar guy once told me "Perhaps it is time to put the covers back on and quit watching them." This was after he was satisfied no damage was being done. He's an experienced Linn-ey. Don't rule this out as possibly the final solution. If you don't hear problems, don't go looking for them. :-)
If this is increasing with volume, Doug could be on to right track. It should be easy to get an idea if this is the problem. If you haven't already tried this, here is an experiment that may help show you something. Try moving your speakers farther into the room at least 4-5' from any wall, back and sides, and see if the pumping decreases.
BTW, what are the room dimensions? Sorry if you previously posted that information. It is possible to calculate room nodes and your speakers may indeed be close to one.
What is the weight of your Universe? I'm assuming you have the extra weight from the little plate.
I seriously doubt that anything you do to the tonearm will fix this without choking off the music.