You've replaced parts in all different systems that will cause all different symptoms. That suggests you haven't diagnosed anything and you're just throwing random parts at it. By now you should have figured out that's the most expensive and least effective way to diagnose a problem. It will be less expensive to get a mechanic involved.
If you can start the engine later without a jump-start, you know the battery and generator are not the cause of the problem. It's rare for a fuel filter to plug so badly the engine stalls, and that won't magically fix itself after sitting a few hours. I don't know how you figured the water pump could cause intermittent stalling. My hope is you replaced all those parts in response to some other problems not related to stalling.
The first thing to do is figure out if you're losing spark, fuel pressure, or both. Unlike many intermittent problems, which can be real frustrating to find, you have a couple of hours to do the diagnosis. If you have spark yet but no fuel pressure, one suspect might be a collapsing pickup screen in the gas tank, especially if you can hear the fuel pump run for one second after turning on the ignition switch. They will stretch out again and allow fuel to pass after sitting from a few minutes to an hour or so. Also, the stalling is not abrupt and sudden. The engine will gradually lose power over the course of half a minute. If you're losing spark, suspect the pickup coil in the distributor is failing. They often become heat-sensitive and work again when they cool down. Since you didn't list which engine you have, it might have a crankshaft position sensor. Those also commonly become heat-sensitive.
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Thursday, March 21st, 2013 AT 11:24 PM