On Wednesday, May 17, 2017 at 5:50:40 PM UTC-4, C-FFKQ (42) wrote:
There's a "Flarm" port on the back of the Zeus, but it's not RJ-45,
like the port on the PF (wasn't planning on using the DB-9 harness that
came with the PF, no idea where to wire it to the Zeus).

Why not? Did you read the manual?

However, the CAN port on the Zeus IS RJ-45, so I connected the PF to
the Zeus using one of my cat5e LAN cables. The PF powers up, updates
and the file it writes out tells me everything is ok.

A CAN bus has nothing to do with the RS-232 connections on FLARM.
You will have been extremely lucky not to have blown up one or
both bits of gear by connecting these two.

Blindly connecting stuff just because they happen to have the
same connector is really, really, really unwise...