[laythea]

Can anyone in the know explain why, if ground clearance due to the new engines is the issue, why Boeing cannot just add a few inches to the wheel stems?

This would raise the whole aircraft off the ground. Surely that wouldn't effect aerodynamics too much as the wheels are up most of the time.

[Glawen]

Because you then need longer and heavier landing gear, which you need to fit somewhere in the plane as they retract. This is a ripple effect where you probably need to redesign the complete airframe, from fuselage to the wings.

They actually cleverly modified the landing gear to gain a bit of heigth, but it was not enough: https://youtu.be/F4IGl4OizM4