Runs rough and sometimes shuts off

When it say ignition coil B do it mean the second coil or what coil is it

The engine starts up okay but when any load is placed on the engine it runs rough. It almost dies when going uphill. When quick acceleration is attempted the check engine light flashes and popping noises can be heard from the engine compartment. The truck will then decelerate and if I pull off the road and turn off engine and restart it will run better for a while. It runs worst between 40 and 50 mph. I have replaced the fuel filter and spark plugs with little improvement.