I would avoid YYZ (especially on the in bound) if your destination that day is the USA; no point in doing immigration and customs twice.

If you fly AA to SFO then fly into JFK (not EWR); all AA's non-stops in NYC to SFO go from JFK. Also, if they are including a business class seat; prefer the 767-300 vs. 767-200; better J seats.

For AUS, it's switched. I would suggest landing at EWR with 9W and then connecting to AA via DFW and then to AUS. There are more flights from EWR to DFW than the once daily from JFK to DFW especially if there are flight delays.

I recall a CO non-stop from EWR to AUS. Perhaps you can book it as a UA flight number if allowed but then you don't the miles on 9W for that segment.