Quick update:
We went for a 26 mile ride on the tandem yesterday afternoon. Prior to this ride, I moved the grips inward by a couple inches per side, effectively shortening the handlebars. This mostly solved the shoulder issue (she commented about just starting to feel a slight twinge in the last couple miles, where before it would start to hurt within a half-dozen miles of the start). The hand numbness/pain was there (but a bit less than before), but she wasn't wearing her gloves.
The hand issues are only on the left side; her right side is fine. I'm going to dig up a good photo of some bullhorns to show her.