this may sound weird but try the fuel cap (i am serious).
this can happen, a car which is suppoed to have a vented cap gets one which isnt or the vent get blocked/ dont work then vacuum builds up in the tank the pump can overcome it and the car seems like it has run out of petrol, later it will start due to air leaking in / fuel vapour filling the void and all is ok then it happens again.
worth a go and not too expensive. i have heard of this happening and people replacing loads of bits on the car then finding this is the cause