Truck runs ruff when you first start in the AM but after five minutes in runs fine.

If all has been done with the secondary ignition components, I would have a "block test" done to determine if the head gasket may be seeping.
Often when the 'rough run' only last for a few minutes of warm-up, the problem is coolant getting on the plugs when they are cold. Once warmed up, the plugs won't foul with coolant.