Looking at your diagram I see a couple things that may cause you problems and reduce your effectiveness.
First, the H-field ant to amp distance - you show it at 3 feet. This is way too long. Whether you are using loops or ferrite antennas here, the wiring from either one to the amp must be as short as possible. That means a couple inches, NOT feet between the antenna and amplifier. The 50ft of Cat-5e between the amp and controller is fine.
Secondly, the E-field ant to pre-amp must be short also. The base of my vertical E-field antenna is connected directly to the input terminal of the pre-amp. The pre-amp is then connected to the amplifier via just about any length of dual or quad shielded RG-6 coax. The E-field amplifier is then connected via a "short" section of Cat-5e cable to the controller board. The ideal "short" section of ethernet cable would be about 1 foot.
Your drawing does not represent these ideal conditions. The 50 feet of Cat-5e cabling for the E-field, as shown in your diagram, may very well cause excessive signal delays and thus, false readings from your E-field data.
Hope this helps you understand more clearly what is needed for a higher quality installation.