After nearly a month I got my wife back on our Burley. A month ago her rump was very sore (bumps not chaffing).
I installed a shock absorbing seat post and put the seat from our old tandem on. She seemed much happier and there were no complaints about bumps.
When we got done (25 miles), she asked why I seemed tired and she didn't. pfft...I told her she was just in better shape than me.
Looks like you analized the sore butt problem correctly!
Nothing better than a happy wife/stoker!
Pedal on TWOgether!
RUdy and Kay/zonatandem