Bogging and hesitating

My van is hesitating and bogging under acceleration. Fuel pump, fuel filter, plugs and wires have been replaced. The transmission was recently rebuilt. There is also a slight whistling noise coming from the engine at idle and at high rpm, like when it is about to shift. I'm out of ideas for this thing. It really feels like it's not getting enough fuel. Sometimes it runs just fine, others it doesn't seem to get the fuel necessary to go, or maybe too much fuel to go.