It sounds like you have a misfire, likely either due to an ignition issue or a vacuum issue. When is the last time the truck has had a tune consisting of at least spark plugs, plug wires, and fuel filter? I think your 1999 is distributorless ignition, but if not, you should add distributor cap and rotor to the list as well.
You also need to check under the hood for and damaged or disconnected vacuum lines and also inspect the tubing between the air filter and the throttle body to make sure there are no cracks in that. Pay particular attention to the connection points as well as between the accordion folds.
-Rod