The online tool only looks at D availability. The QF website looks at any of the J fare classes.

I've never had issues getting D on SYD-NRT. If you can't find a D seat on QF21, try JL772.

Are you wanting to stop in SAN, or is that to try a 787?

You could try
CX: LHR-HKG
QF: HKG-SYD
JL: SYD-NRT
AA: NRT-DFW or JL: NRT-ORD or BOS (if wanting 787)
AA: DFW-MEX (or from JL ORD-MEX or BOS-DFW-MEX)
BA: MEX-LHR