Chris, The trailer wiring is normally connected up under the trunk. You would remove the panel under the trunk (4 screws).
There is a Red connector at each rear corner where the trailer wiring harness is connected in series.
This is how it is normally wired but who knows how yours might have been connected.......!!
Did you replace the Tail Main Relay # 3 and check its contacts.....??
That relay always has "load" power (even with the ignition OFF).
If by chance you did something to short the "coil contacts" on that relay together, you would have a drain on the battery (even with the ignition OFF). And a lot more drain when the ignition was turned ON.
This was one of my thoughts earlier on so I swapped the tail/main relay for one of the others in the relay box (I don't have any spare relays to hand) and it was still the same. I'll take the top box off in the morning and check out what the wiring is like for the trailer. Is there any way I could check the operation of the relays while I'm at it do you know?