Last weekend I got the firmware to a state where it could be used in the aircraft and installed it all into the pod... Not very pretty, but it'll do for now.

During my pre-flight checks I noticed that the radio was picking up interference (the SQL had to be set all the way up to suppress it); Upon closer inspection with the oscilloscope I noticed that the switched mode power supplies were ringing around 100 MHz during both the rising and falling edges... Additionally the Microchip PIC is set to run at 119.763 MHz. The capture below was taken with a floating probe around 5-10cm away from the SMPS.

Re-wiring the electronics with shielded cables (and connecting only ONE side of the shield to ground) fixed the issue. It's clear that each of the modules as well as all interface cables should be properly shielded to suppress their emissions, and shield them from the VHF radio and transponder RF!