Runs rough and sometimes shuts off

It sounds like the coil itself is breaking down. Have that checked, but I think that is where your problem is coming from.

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

Yes

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.

Check engine light coming On.

You need to scan the computer for code/s there's a problem within the engine management system this is your starting point of diagnosis

Try and get a code from computer may provide clue to what's going on.