Small displacement measurement of a conducting beam with Neodymium magnets
You mentioned:


  some form of optical sensor probably based on intensity with fiber wires for the sending and receiving light using some form of modulation and filtering


This is a good idea. You can do very precise measurements with lasers, measuring phase differences to get distance. This is sometimes done with the laser wavelength itself to get micron resolution; for larger resolution and range, you modulate the beam to a specific wavelength.
I'm not sure I understand the application entirely, but it seems like you will be measuring two different points at the same time, each with a different range. For a certain range, I would choose a wavelength at least 4x that -- this sets a maximum modulation frequency. For example, c/(4x6cm)=1.25GHz for the end of the beam. (You can use a much lower frequency, too). Resolution has a theoretical minimum set by the wavelength as well, but will be practically set by your detection setup. The idea is to compare the reflected phase with a reference.

Here's how Brad did it to pick up minute sound vibrations on surfaces far away -- a laser spy device: http://www.lucidscience.com/pro-laser%20spy%20device-1.aspx