I heard that the stop in TIJ was canned because the airport is ill equipped to handle customs and immigration, making for a poor overall experience(though they still do the stop for the PVG-TIJ-MEX flight as there is a bit more demand). The poor facilities, coupled with the few passengers who boarded/deboarded at TIJ from NRT caused AMX to skip TIJ altogether on the way back from Narita.
They're currently upgrading the terminal building to address some of these issues so let's see how it goes.
As far as booking the flight, I sometimes had trouble getting the flight to show up, even when it stopped in TIJ both ways, AM's booking engine is just plain wonky. I also just tried searching for flights with no luck.
You might have better luck calling them, I was trying to redeem some tickets on KE with my Premier km's and the agent was offering me the AeroMexico flight from TIJ to NRT and back through MEX.
That said, if you do succeed, remember you'd be stuck on a 767 with not much in the way of IFE in either Y or J.