Multimode cavity resonator
As has been mentioned in the comments, the resonance modes in your box will not be predictable and will be different for an empty container than for the container filled with pallets and will vary when you insert your goods on the pallets. Even if the goods would always be the (nominally) same, the modes probably will vary from shipment to shipment.

There are several ways you can figure out the solution: 1) simulations, 2) measurement with a probe, 3) building your final setup with goods and everything and trying it out. 

I have only used CTS and HFSS, but I found some possible tools that you might want to try: MaxFEM, emGine, deal.II, Hypre. I have no experience with any of these, they are just what seemed promising after some googling. Even if the simulations aren't perfect, they might help you visualize a lot while varying only one input parameter.

The measurements will be difficult because your measurement setup will disturb the setup. So one route might be to minimize the disturbance as much as possible and hope that it would be enough.
I have sometimes needed to measure currents that are induced in conductors in the near field. That measurement has similar challenges as yours: if I make a probe and connect it to the measurement equipment, the current in the cable completely messes up the current that I try to measure. One solution that I have been thinking about would be a small loop as a probe, possibly tune it near your frequency with a capacitor, use Schottky diodes as amplitude detectors, add an op-amp as a current driver, modulate LED intensity with the current, steer the LED light through optical fibre, and de-modulate outside your container with a photo diode. After that, you can move your probe inside the container while transmitting with the antennas and see how the intensity varies.

Full disclosure: I didn't build the system and there might be some issue that makes the idea completely nonsense. Good luck, let us know how it went?