I stopped by the PT Cruiser forums and no one there could help, so here it goes.

Her car runs like crap on a full tank and less than 1/4 tank. Anywhere in between it's fine. It acts as if it's be starved for fuel, sputters (but stays running) while accelerating, rough idle too. The pump and filter are in the tank, which I can drop this weekend - but wanted to see if you guys and gals could think of anything else it could be.

 

WAG: Evap system? Any CEL? Clouds of gas fumes on hot days? History of overfilling the tank?

Otherwise, I think you are on to it with the pump and filter.

 

You could watch fuel trims while it's running bad -- see if the computer agrees that it's lean. You didn't mention a CEL so I wonder about that.
Not sure what that would mean, but it's odd.

Other thought would be some kind of a double problem -- evap getting stuffed with fuel after fill up and crud in the bottom of the tank that only causes issues when fuel is low.

Only guessing -- good luck!

hj