Don't bother looking at the depth or wind as they aren't connected via the Fastnet bus.
It sounds like your system has only four nodes on the Fastnet bus - two FFDs, the Halcyon compass and the Hydra processor, is that correct?
You talk about "taking off the wood cover" - is that some piece of your boat's furniture?
It really sounds to me as if it's a wiring problem. Take a close look at the wires - was the installation done with stranded wire or is it with solid core wire? Solid core wire is notorious for breaking inside the insulation and becoming intermittent while looking pristine. You don't need to use "B & G" cable, but if you have solid core wire you should remove and replace with stranded cables.
When is the last time you did a full system reset of your Hydra?