Wider stoker bars. With her hands on the forward part of the bars, her fingers should still clear your thighs/butt.

Set the stoker stem and stoker bar height to what is comfortable for stoker. Make it as much as possible like her single.

New discs or pads do suck. It will take them a little while to bed in. Meanwhile, give yourself a little extra distance. You can speed the process by riding hills and stopping at the bottom.

And what twocicle said.