The iPod interface module needs 7 wires connected to function: CAN +, CAN -, power, ground, ipod right, ipod left, and ipod shield. The latter three are done by connecting the module's harness to the 35 wire harness already on your bike. If you check the wiring diagram for your bike, you'll see that chambers 8, 19, and 31 are not used; they'll be used when the wiring from the ipod harness is connected to them.
The ipod power, ground, and CAN + and - would normally be supplied via connector 6 using the ipod harness, but since your connector 6 is not compatible with the connector 6A supplied with the kit, you simply need to tap those wires in your connector 6: CAN + = yellow/orange wire, slot 1; CAN - = yellow/violet wire, slot 2; power = red/orange wire, slot 3; and, ground = black/green wire, slot 6 to the iPod harness.
I'm not a tech or audio guy, and I haven't done this particular install. But I have studied the wiring on these bikes and confirmed that this approach works on the SESG2 for XM, and you are experiencing the same problem with the wiring connector that is encountered with the SESG2, so the same solution is provided here but in a modified form since the accessory is the iPod module and not the XM module.
Carl