So I took the following steps and the cannondale and her power went up and extra comfort to boot.

Bought Chinese carbon flat top tri base bar and wrapped it.

Used a plumb after marking her leg with a sharpie on her road bike. This lead to a one inch setback being needed on the tandem. -- pushed her saddle back.

Switched back to the regular control tech extended stoker stem.

Measured her bar position better relative to her road bike and matched the drop

Her position is now 1.5" shorter than her road bike.

New titanium setback post and saddle similar to her road bike is on order.

Did 55 miles today and she was much more comfortable.

Interestingly I had much more control while she was mashing and bumps were less of an issue for us both. I'm wondering if the carbon bars took some of the body motion out of the stoker compartment and absorbed some of the impacts.

My position is better because I don't have a stem in my butt any more.

Thanks for the tips on the stoker bars and setback of he saddle.