Jonathan Goodish wrote:
I flew the airplane today,...The "chop chop" or "flutter" electrical noise is
still occasionally present in the system when the copilot transmits, and
can be heard in the sidetone.

The "chop chop" sounds like RF is getting into the mic audio line, and
is causing what hams call "motorboating" (The RF is rectified in the
intercom or audio panel input circuits, the resulting DC bias shift
causes the low-frequency oscilllation).

Solution is to prevent the RF entering the audio line. Put a 100pF RF
bypass capacitor at the Mic jack between either:
1). the Mic line terminal to the floating common terminal, or
2). " " " " to airframe ground near the mic jack.
Try 1) and 2) to see which accomplishes the desired result.

The question is why is RF floating around inside the cockpit. At other
things working properly, this is not supposed to happen. A bad Com
antenna (bad coax, oxidized BNC connection, bad RF ground between
antenna base and airframe) can put a high VSWR onto the Com's transmit
coax, and cause radiation off that coax so that it couples into other
nearby wiring. Fix the antenna, the VSWR returns to normal, and that
gets the RF out out your audio.