Are these award tickets using AA/BA miles? Can you issue one-way travel on CX in F and maybe Y in another carrier through TYO if you want to avoid the shell seat in CX Y? And it will break down the travel by a bit so you can walk around for a bit and relax at the lounges before your next flight
If it's not an award flight, would it be better to go through TYO in either inbound or outbound and use whatever AA upgrade coupons you have to upgrade that transpacific flight, and fly on either JL or CX codeshares to/from HKG in Y?