Make the ground plane of pcb part of the Faraday cage and bond it to the cage at as many points as possible. The signals passing the Faraday cage should do it via pi-filters, with their caps at both sides (inside and outside) referenced to the ground plane directly at the Fraday cage. The signals are fed through the Faraday cage via ferrites or resistors. Make tiny holes in the Faraday cage, where the signals enter or leave it and place the series element of pi-filter directly under the barrier.

This would be optimum. But you might not need caps at each signal line in any case. Even only resistors or ferrites might help. But they must be placed directly at the barrier, with one leg inside the Faraday cage and the other leg outside. Only then they make sense.

Feedthrough capacitors is not a good choice when having SMD components on the pcb, but might also work. Unfortunately they are extremely expensive...

Kai Klaas