But hey, IANAP.
Yes.
> When calling this a temperature below 0K - isn't this shoehorning the concept of temperature onto something it wasn't meant to do?
No. Suppose you're doing a Fluid Dynamics Simulation. You need to assign a temperature and pressure to each point in space to simulate gas flows. Using the negative temperature will correctly predict the evolution of the gas flow.
This is actually a strength of physics, having equations that can take on values that to your knowledge are unphysical (such as negative refraction indices for example) but still work. This means that when someone manages to figure out how to build such a system; we don't need to rework all of our theorems (conservation of energy; momentum; etc) to see which are still valid. We also have the ability to investigate the applications of such materials; should we ever be able to find a way to create them.
http://en.wikipedia.org/wiki/Metamaterial
> Isn't this transition from a positive temperature to a negative temperature system non continuous, as in it needs to be set up with different properties
There are plenty of discontinuous transitions in thermodynamics, phase diagrams are an example. This is hardly an argument to that the concept of negative temperature is a broken one.
As for discontinuities, another non-thermodynamic physical discontinuity is the speed of light. Special relativity predicts it's entirely possible for particles to move FTL, when it's actually crossing the boundary that's a problem.
[0]: http://en.wikipedia.org/wiki/Plane_wave#Complex_exponential_...