Is there any chance that you still have the old pump assembly? I'd compare the pump and pickup tube shape on the old and new parts. If they're not the same, you might be able to swap the new pump onto the old assembly.
If they're not close to the same, especially if you can't swap the pump over, then you were sold an incompatible part, and should get a return or exchange. I'd also double-check their website and see if that part number is listed as compatible with your truck. Of course, this assumes you have the correct factory tank and that it's not damaged or misshapen; if you have a different tank it's your responsibility to request the corresponding assembly.
I've had a guy at O'Reillys sell me the wrong starter solenoid, even after I asked him about the different mounting flange. I later that day looked it up and found _their own website_ listed the other part for my vehicle, and not the one he sold me and insisted was correct. (I'm certain they use the same parts database for their outside website and their store-counter lookup.)
Alternately, there's a distant possibility that when the frame flexes that direction it pulls on the wires or connectors and causes a short or disconnection, but it doesn't make a lot of sense that it would only have an effect when the fuel level is low. I'd only pursue this possibility if you determine that the new assembly is definitely correct.