2001 Chevy Malibu the car cranks but wont start I can hear the whine of the fuel pump coming on when I engage the ignition switch to on position, I can prime it and it will run for a few seconds but once that fuel has run out it quits is this possibly a clogged fuel filter?

If you hear the fuel pump whine there is no fuel cut off switch .Your best bet , have a qualified repair shop check it out . You have no clue how to diagnose . Looking at wiring diagrams to see what all is involved in the fuel , ignition systems , checking to see if there is spark at the spark plug's , checking fuel pressure . So do yourself a favor . Takes special tools an service repair information to diagnose newer electronicaly controlled automobiles .

I just have one suggestion, after what all your mechanic already did. I would want to know the fuel pressure reading WHEN IT WON'T START. So you would need a fuel pressure gauge handy, for that time it won't start. Hook up the gauge and turn the key on- if at 59 psi, when the engine won't start, then you know the fuel pump and the relay sensor is not the problem. And so probably not a fuel problem, although you haven't checked the injector circuit, but likely that wouldn't exhibit a problem as you have.
So if not a fuel problem, check for spark when it won't start. Maybe the problem is in the ignition system. Buy a spark tester from a parts store, use it when the **** engine won't start- simple and easy check of your ignition system.

you should check the battery, if it is all right, you should try to check the starter and ignition.
_____________
Launch X431

Start with the fuel pump.When you get into your car turn the ignition key to the on position but do not start your car.Listen for the fuel
Pump to engage,you will hear a low whine.If you hear the pump engage,that doesn't rule that the fuel pump is fine.It sounds like the pump though.

sounds like a bad solenoid on the starter. replace the 1999 starter(Its old).

check connections from the battery to starter if ok tap on the starter with a hammer as a helper starts the engine if it starts replace starter before you do dose the key turn all the way forward normal starting position? reason i ask is why did you replace the ignition cyl lock?

the first item to ck is the ignition switch

sounds like a fuel pump problem. take off gas cap and have someone sit in the truck and turn iginition key to on. (do not turn key as if you were starting but to "on only") you should hear the fuel pump engage. if you dont hear the fuel pump then check the fuel pump relay. it is located behind the glove compartment. hope this helps...

iam not sure but the most common culprit is a bad ignition switch. if the switch goes bad then no power will get to the gauges etc. check switch.

Does the starter make any noise or click when you turn the key to start? If it does not, chk. battery could be bad, and battery cables could be loose or corroded. If there good and clean and battery is good try tapping starter see if it will turn and start if it does or still clicks starter bad. It could be ignition switch if it does nothing at all, but if it clicks most likely its starter.