Not sure what you mean by the (bne) included between SIN and NRT. Do you mean the NRT-BNE-SYD route? If so, then that flight is not available on a xONEx fare since it is operated by JAL and only a QF codeshare. QF operates direct NRT-SYD flights (one daily non-stop, one daily via CNS and one weekly via MEL). You cenrtainly cannot transit BNE between SIN and NRT.

Also there is no direct flight JFK-BKK. You will need to transit either HKG (CX) or NRT and HKG (AA/CX), but that is not an issue with the routing.