Car won't start

We have a 1999 Mercury Grand Marquis 4.6L- recently the car wouldn't start. We have changed the fuel filter, fuel pump and the fuel pump relay. The car starts now, but it will not stay running. It "bogs out" after a minute or so. If we give it gas, it turns off right away. A day or so later we went back out to try and turn it on again and the battery was dead. It's a newer battery. We think it has something to do w/ the changing of the fuel pump. When we removed the gas tank, there were two screw holes in it due to an after market amplifier being put in (they screwed it to the gas tank, by mistake) we put some JB Weld on it to seal the holes. Any suggestions as to why it won't stay running now? (Fuel pressure or sensor. Maybe?)Please help, it's our only vehicle.