I am stumped. The CM is supposed to land Nose up. So Y is up. for the cockpit and such I think the vessel needs to travel along the Z axis. But can it land with the stern down?
How do you know if in the VC?
The concept is called a "tailsitter", and there are a lot of examples of it in various orbiter add-ons (I remember one from the 55 Cancri system, for example).
Yes, your axis of thrust should point along the Z axis. You have to set your touchdown points prallel to the Z-axis too. Tailsitters are a bit hard to land, but far from impossible. If I remember correctly, LOLA-Mfd even had a tailsitter landing autopilot.