Seeing as how Starthaus is done with this thread, this is a question for Rasalhague.
Do your equations agree numerically with the following simple trigonometric analysis?
Consider two frames S and S' that have relative velocity v/c=\beta and axes aligned with each other when there origins coincide and S' is moving along the x-axis of S. (We are always free to align the coordinates frames in such a way that this is true.) The rod is at rest in S with proper length L and one end at the origin and the rod is orientated in at an angle (theta) in the x,y plane. (Again we are always free to align the frames this way.)
In frame S' the angle (theta') of the rod relative to the x' axis is by simple trigonometry and allowing for length contraction is:
\theta' = \tan^{-1}\left( \frac{L_y'}{L_x'} \right) = \tan^{-1}\left(\frac{L_y}{L_x \sqrt{1-\beta^2}}\right) = \tan^{-1}\left(\frac{\tan{\theta}}{ \sqrt{1-\beta^2}} \right)
The difference between the two angles (phi) is the "rotation" of the rod (The Thomas rotation) and is given by:
\phi = (\theta - \theta') = \theta - \tan^{-1}\left(\frac{\tan(\theta)}{ \sqrt{1-\beta^2}}\right) \qquad \qquad (Eq1)
This rotation angle is independent of the orientation of the axes with respect to the motion or the rod, and only depends on the angle of the rod with respect to the motion.
In the earlier example I gave the equation for the rotation as
\phi = (\theta - \theta') = \theta + \tan^{-1}(\cot(\theta)\sqrt{1-\beta^2}) - \pi/2
when the rod was aligned with x-axis and the motion was at angle (theta) wrt the x axis. It is easy to see that the two equations are equivalent because of the truth of the simple trigonometric equality (at least when 0<x<=1):
-\tan^{-1}\left(\frac{\tan(\theta)}{x}\right) = \tan^{-1}(\cot(\theta)x) - \pi/2
Now for the length contraction aspect of the problem.
In frame S' the length of the moving rod is given by:
\| L ' \| = \sqrt{L_Y'^2 +L_x'^2} = \sqrt{L_y^2 + L_x^2 (1-\beta^2)}
In the rest frame of the rod L_y = \tan(\theta)L_x so the above equation can restated as:
\| L ' \| = \sqrt{\tan^2(\theta) L_x^2 + L_x^2 (1-\beta^2)} <br />
= L_x \sqrt{\tan^2(\theta) + (1-\beta^2)}
It is also true that in the rest frame the x component of the proper rod length \| L \| is given by L_x = \cos(\theta) \| L \| so the equation can be further restated as:
\| L ' \| = \| L \| \sqrt{\sin^2(\theta) + \cos^2{\theta}(1-\beta^2)} \qquad \qquad (Eq2)
Again, this equation is independent of the orientation of the frames wrt the motion or the rod. It is easy to check that when the rod is parallel to the motion and theta=0, the equation reduces to the familiar \| L ' \| = \| L \| \sqrt{(1-\beta^2)} and when the rod is exactly orthogonal to the motion and theta=pi/2 the equation reduces to the expected \| L ' \| = \| L \|.
In summary, the rotation (Eq1) and the length contraction (Eq2) is only a function of the angle of the rod wrt to the motion and is independent of the orientation of the axes wrt the motion and independent of the orientation of the rod wrt the axes. The only limitation is that the equations require that the two frames have their axes orientated in the "standard way" (See
http://math.ucr.edu/home/baez/physics/Relativity/SR/velocity.html). In practice this means in our case the z axes remain parallel to each other and the x,y planes remain parallel to each other. This slightly awkward definition comes about because when motion is not parallel to the x or y-axis the x and y axes themselves appear to rotate from the point of view of frame S'.