The mass air flow sensor, the throttle body and the idle air control motor need a good cleaning. Use a brush and brake clean everything except the Mass air flow sensor, just spray it down, both sides. After you clean it, it will take a few second to restart.
SOURCE: 2002 Ford Taurus ses 24v DOHC
Sounds like when you ran the car out of gas the fuel pump was damaged, these in tank electric fuel pumps are very small and produce allot pressure and volume, the way they do this is to use the gas around them to cool down, when the pump comes out of fuel when the tank is below 1/4 full it starts to get hot very quickly, since your pump was well used (109000 miles) that was the last straw. When you replace the pump also replace the fuel filter.
I would also clean the throttle valve and idle speed control valve, this may be contributing to the low idle complaint, clear the system after the pump and cleaning by disconnecting the battery for a few moments.
SOURCE: idle control
tps (throttle position sensor) controls the idle and the ideal idle is around 700-850
SOURCE: 1990 Toyota Celica GTS. Idle races too high
sound very much like a vacuum leak.... also maybe your timing is off? possibly advanced? try retarding it with the distributor if thats the case...
SOURCE: low idle stalls out
Here is the most common cause of surges and stalls at stops and low erratic idle speed and rough idle, it is the idle speed control air-bypass valve and throttle valve (IAC for short), they get full of gunk over the miles and cause idle issues (stalls, low idle) like yours, Get a can of intake cleaner from any local parts store, not carb spray, intake cleaner, it is made by a company called CRC, remove the air intake hose to the engine, hold the idle high so the engine won't stall, then spray the can of cleaner into the intake while keeping the engine running, use at least 1/2 the can, shut down the engine and disconnect the battery for 5 minutes, then restart and complete a number of mixed driving cycles, town, freeway, stop and go etc., after a few days the problem will go away as the system will relearn to the clean intake.
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