Took some time to glance at the 16 FSM for the Fronty...
Obviously, the control head and the evap/heater core. Probably the duct work as well. As for details, bits of harness between the controls and the core, ambient air sensor, in vehicle air sensor, maybe even some dash components to account for the new duct work and core. The big question will be how the BCM and ECU in the X responds to the new HVAC controls. There are a few lines between the HVAC and the BCM in the X, but the Frontier has more, and one set has some sort of optical sensor on it.
The physical/mechanical aspect of this mod is one thing I cannot figure out without having both vehicles present. I'm assuming the coolant and refrigerant lines are very similar between the two models, since there is a good deal of history between them, but since the Frontier is designed for a two person cab vs. the Xterra with a 4 person, there may be differences in fittings.
It may not be as bad or outlandish as originally thought, but still a good amount of (expensive) work.