2000 Ford Expedition sat two years. Drained fuel, replaced fuel filter, new fuel pump. SUV runs rough at higher speeds starting about 40. Any suggestions?

 

Had a very similar issue with a '99 Explorer I bought for my sister, but worse.

In addition to what you have already done, I had to replace the fuel tank because it was full of rust, but your tank should be plastic, so that's one good thing.

Turns out there was some rust in the fuel line that had clogged the fuel injectors. It was very obvious once the fuel rail was removed. I removed the injectors and sprayed both sides with throttle body cleaner and it's been running great ever since. Without having the vehicle in front of me, this is where I'd start.

Also check for vacuum leaks and rotten hoses. Replace any that are rotted, hard, or brittle.

There are other things to check such as plugs, wires/boots, and I'm assuming your check engine light is off since since you didn't mention it.