Q:

Z values way too large compared to x and y in reconstruction

I reconstruct x,y,z from disparity using  triangulation formula .My problem is that x,y, and z  values are in very different orders .For eg order of x is like 0.001 and similar for y but z is in the order of 10 .Because of this I see a straight line instead of seeing a face .Is there any way I could apply some transform preserving the structure of face but getting a better reconstruction.
EDITED: here is a sample L image and the disparity map ( normalized to 0-255 for visualization not the true values).My point of giving this is to show that disparity comes out fairly decently.

A:

Assuming that you are solving for the fundamental matrix using point correspondences between the left and right images, this is the expected result. Because the fundamental matrix is rank-deficient, it is only defined up to a scale factor. If you define everything in terms of pixel units, there is no way to reconstruct the scene in real-world units.
Solving this requires an additional piece of information: the relationship between a pair of corresponding points in a three-dimensional coordinate frame. For a stereo system, this is most often the baseline, the distance between the left and right camera centers.

