Since the engine fires with starter fluid - suggests a fuel problem more than an ignition problem, as you've already suspected.
One possibility is that the pick-up screen in the tank has become plugged. Suggest to get a reading on the fuel rail pressure to see if fuel is making it to the injectors. There is a Schrader valve (like a tire inflation valve) on the rail to check the pressure.
Also, this valve can be depressed to see if fuel comes out - but be careful, may be upwards of 40psi that will spray everywhere, not to mention the hazard of atomized gasoline floating around.
Another possibility is that there is an electrical problem, such as a failed ground, that is not allowing the injectors to fire.
As a note, many vehicles will shut-off the injectors if a wide-open throttle (WOT) is detected during start - but that wouldn't explain the stalling while running.
As a final thought - if you've replaced the fuel filter after the stall, then you need to make sure the fuel lines are purged. This can be done by rolling the key from OFF to ON several times, letting the fuel pump do its short-cycle run each time and charge the lines - usually about 10-15 times will do it. You may hear an odd 'whooshing' noise as the air is pushed back to the tank.
