Won't start...maybe fuel pump??

I have a '99 windstar 3.8l engine. The problem i'm having is that the engine periodically cuts out. If i let it sit for a while, it will start back up. This has happened 4 times in the last month. This last time, the van sat over night in a parking lot and still won't start. I've been told several things, when i turn the key i should hear the humming noise from the pump pressurizing, the fuel pump is bad, the relay switch is bad, the chip in the key is bad. I've been told to try banging on the fuel tank and tried 3 other spare keys and still won't start. I have a problem with mice in my garage eating bird seed and i have found bird seed shells throughout the engine compartment. Now i'm thinking that something has been chewed on. The van was towed to my local mechanic. He could not find any chewed / frayed wires. In the box where the relay is located, there are 3 other relays for other functions that are exactly the same as the fuel pump relay and he swapped them all around and everything still works fine but still won't start. He even replace the relay. He is only geting 6 volts to the pump and it need 12 volts to run. He pulled the relay out and put a jumper (a small piece of metal wire) in the recptical and it starts just fine. He said that there is no ground from the pcm to the relay and possibly the pcm needs to be replaced and flashed, which he can't do. So now the van has been at the dealer for 2 days. First, they told me that it keeps blowing the relay. I don't see how this could happen since the other relays were swapped into the pump relay location and they still work fine in their original locations.
Now they are telling me that the fuel pump is overheating and is shutting off. Well, if that is the case, why won't it start after sitting over night?... Why does it run fine with the jumper? Why does the jumper accept the ground and the relay does not?
I'm sorry that this is so long but i had to explain as good as possible. Any information would be greatly appreciated!!

I have more questions than answers, but hopefully these questions will help you understand the problem better.

Does the dealer confirm the low voltage reading at the fuel pump? If so, then where are the other six volts being lost? Is the dealership able to start it when there is a jumper in place of the relay, like the mechanic found?

If the relay is being burned out, then that suggests there is a current over load, possibly due to the pump. How much current is the pump attempting to draw through the relay, and is that within specificiations? If the current is more than expected, then is there a problem with the pump, or is there a short in the wire between the relay and the pump?

When you mentioned "Only 6V" at the pump connector...at the fuel tank....I thought bad connector.
Now when you say that the dealership is saying that it is burning out relays......I am thinking high current draw as tomj76 mentions.

So....I wonder if a measurement each side of the relay is in order.......6V on the pump side and 12V on the supply side?

If you have around 12V on both sides of the relay....then I would move back to the back.....in the jack compartment.....and check the inertia switch.
I have seen a post or so about them failing (not common).
The inertia switch is supposed to shut the fuel pump OFF in a accident.
Worth checking.

I am not getting where the PCM will cause the fuel pump relay to burn out.
The wiring on the 1999 is somewhat different than my '96, there is a connection to the PCM on the pump side of the relay contacts......supposedly to sense that the pump is activated.....but I don't think that they utilize that function in the firmware of the PCM (as we don't seem to get any code(s) when the pump is not activated).

The 12V input to the relay contacts is protected by a 20A fuse (Fuse N in the engine compartment fuse box on the 1996 windstar).

In short.....when one can duplicate the low (6V) at the pump connector......that is the time to back track to see where the voltage drop takes place.
I am leaning toward that inertia switch.....or dirty/corroded connection/contacts someplace.
I would think that current that would burn out the fuel pump relay in short order would blow the 20A fuse.

DO NOT drive with the relay jumpered out.....
In the event of an accident (we never plan for one of those), the fuel pump would stay running.....feeding fuel to the engine compartment......which can result in a nasty fire.....that has fuel constantly fed to it.

First of all, thanks for you input / information!! The service guy at the dealer called me yesterday morning and said that he is convinced that it is the fuel pump and that he would not doubt his mechanic, but he could not explain why he was so positive about the fuel pump being bad??? His only explanation was that the bad fuel pump was blowing the relay. I told him that i was not convinced that was the problem. When i picked up the van last night and met with the service guy that help me originally and he was very helpful. He explained that the fuel pump was overheating and shutting down. The last time it shut down, the pump must of had too much resistance and popped the relay fuse which is a 15a. The fuel pump relay is fine. Now this makes sense to me and up to now, the fuse was never thought of or mentioned by eighter the first shop or the dealer. The jumper was bypassing the fuse. The dealer wants almost $900 to replace the pump and the trade-in value is only $1400. The other problem is that we were getting ready to do a trade-in when this all happened. If i keep a handfull of 15a fuses in the van and just run it as-is, will this cause further damage or just prolong the life of the pump?

Dropping that fuel tank is a bit of a pain. I've done it ... not fun! I think I paid about $350 for a fuel pump from Ford Parts desk. Bet an aftermarket pump would now be much cheaper. And you could find a neighborhood garage that would change out the pump (be sure to have the inlet screen included ... you may have to buy separately) for a reasonable price.

I would keep the tank topped off to help dissipate heat and lessen chances for fire until something is done/traded.

Yes.....a bad fuel pump is very likely......I neglected to mention it....but wanted to eliminate the other, less expensive and labor intensive possibilities first.....
I was focused upon the PCM idea....which did not seem to make sense.

Y2K ford in Seattle lists the fuel pump for your 1999 at $239.22 vs a suggested retail price of $346.70

Rockauto lists the Motorcraft pump at $277.79
They list the Airtex at $194.79 for the complete assembly.