[Sirrotica]

Running it out of gas can clog the injectors with all the crap that accumulates in the tank. There is a fine sock where the fuel rail attaches to the injectors about 3/16 inch in diameter. It sits down inside of the injector and can be removed and cleaned. It is the final place to stop contaminants before they reach the injector tip. I have seen these plugged solid with sediment and stopping the fuel flow to the injector. This is a possibility given you ran it out of fuel before all this missing started. You might check there first. Remember you have to have 3 ingredients to fire a cylinder, fuel and air, compression, and spark. Missing any one of these will cause a miss. Do a systematic search and you'll find the problem.