eliminate noise pickup from shielded enclosure's surface
You likely have a ground loop in your setup. 

I have a bit of a hard time following the description of your setup, but if you can illustrate your setup in the form of a grounding diagram, I would be willing to get into more detail with giving you specific advice.

The bottom line is that there are two keys to minimizing EMI (electro-magnetic interference) in your setup:


Ensure that your entire setup is enclosed in a continuous faraday cage. This will shield your detecting elements, amplifiers, and wires that may act as antennas from EMI.
Ensure that the faraday cage is connected to your signal ground at only one location. You can experiment with exactly which location works best. The purpose here is to  ensure that return currents travel through signal grounds rather than through the faraday cage.


Wikipedia has a good article that may help you understand ground loops here. 

It may also serve you well to use differential signaling on any long cables that you have. This would involve using something like the AD8138 for driving analog cables along with twinaxial cables or for digital signals using LVDS, RS-422, or similar signaling method.

One more piece of advice: Make sure you are using a linear power supply as opposed to a switching power supply. Switching supplies, while more efficient, can contribute to noise in your amplifiers through the supply rails.

Good luck!