I'm interested to find out if you found a setup that worked for you - as, based on my experiences with tyre pressure, I would have thought good tyre pressures would have sorted it out.
On the issue of tyres... runflat tyres have more 'substance' to them - so presumably they'd be heavier. Could this account for some of the differences you're feeling? I would think a lighter tyre/wheel combination would move more in response to bumps, but overall I think many have previously found a more comfortable ride on conventional tyres.
It is a puzzling one...
All the best,