OK, I will answer this question myself since I think I should have solved it:
There is an algorithm for 3D reconstruction based on cuboids/cubes described in this paper:
So what I did is first to "estimate" a 3-d cuboid form based on the known positions. For this I estimated and averaged x, y and z vectors. I got the z-vectors indirectly by constructing a point p' that would lie exactly above the points in the gouges of the plate like this:
So I got two artificial cubes based on the top and bottom image and got the average side lengths of the cubes in 2D like this:
From there on I could follow what was described in the paper and created an first version of the 3D shape:
As this was still far from optimal, what I did next was to create a 3D grid of real "world coordinates" and minimized the error between the reconstructed 3D points and the real points with a function like this:
[squareError] = optimizeWithGlobals(F)
refinement with fmin-search
Refined_F=fminsearch(@optimizeWithGlobals, ForRefinment_F, options);
I also took some measures to prevent it all to get stuck in local minima. and got a good reconstruction in the end (green x-es are world points, red ones are reconstructed):
Notice that some of the points on the edge are a little bit off (but none more than 0.2 mm). This is mostly because I could not set these points as precisely as the others in the grid image (was fixed later):
Also a special thanks to Michael who helped me with some advice on how to optimize my reconstruction
If someone wants to know more details about this approach, it will probably be explained in more detail in a future publication (I will link it here, if I remmber it). Also, there is always the option to comment here with questions (but do not expect fast response times).
Edit: I forgot to mention that this whole process is used to ptimize the F matrix that is basically the "function T" I mentioned in the original question:
T(calib2D_bottom, calib2D_top) = calib3D | T=?
so with this F matrix I should now be able to reconstruct surfaces as long as the recording settings stay exactly the same.