CZRY did run a train in the Gorge that all I can say was nothing more than a publicity stunt. It consisted of some double stacks and auto racks that UP delivered to Plaster City. They did run a ways up the Gorge. At the time (IIRC), there were some blog posts claiming that they immediately ran into clearance issues with the double stacks at the first tunnel, backed down and dropped the stacks, and tried to continue with the auto racks until they damaged them a few tunnels further. I was working in the area at the time and knew of their intentions, so hiked a little ways in (Dos Cabezos?) and did get some photos - presently lost. So basically there never were the required clearances to run autoracks (there was a lot of noise about the expected Toyota assembly plant at the time) or stacks through the Gorge. This would have been circa early 2005?

The SDA was built with mostly 75# rail and native decomposed granite for ballast, which is pretty much still there. The entire line, rail, track structure, tunnels and most wood trestles would have to be completely replaced to be able to handle 286k, stacks or even autoracks. SP/SDAE and Kyle's SDAE both did handle piggyback into San Diego on standard pig flats (not sure how they made it around some of the curves), so it would be theoretically possible to reinstate intermodal service using spine cars without improving clearances.

The Mexican Government has done preliminary surveys to connect Tecate to the Port of Ensenada, and there was an option to continue an all Mexican route to Mexicali. The SDAE and Port of San Diego still suffers from the basic geographic disadvantage of being in a corner. Traffic patterns would really have to change to justify rebuilding the SDAE to move traffic east through either Mexicali or Niland, as pointed out the old Inter-California would have provided a better option for traffic going east by connecting near Yuma.