From what I recall the connectors are the same, assuming that is correct...
I would start out worrying about the connector that goes to J1086 (master, on the right hand side of the vehicle) only.
You need only the following there to get the system show up on the can bus...
Pin 3 - Extended can high
Pin 4 - Extended can low
Pin 5 - Ground
Pin 8 - Power
Even if you don't code anything VCDS (and I suspect OBD 11 although I don't know) should see the module on the CAN bus and allow you to select it.
I don't remember which part number should be J1086 but you can try plugging in both because they both receive power/ground on the same pins. And as
@xabhax said, swapped can lines won't break anything, you just won't get communication.