Clogged air filter or blockages in the air intake tubing

Clogged fuel filter

Clogged fuel pump filter:

If you have a clogged fuel filter pump and a lot of debris in your fuel tank make sure to carefully inspect the fuel tank and hoses for cracks ,chips and hole. All that debris had to have a way in.

Fuel pump problem:

could be a dieing fuel pump or and electrical issues , i.e. pump shorting out , pump not getting proper voltage , ect. For more information on fuel pump issues click here.

Blockage in the catalytic converter:

as cats age and build up debris they can sometimes become clogged and choke out the engine as the exhaust can not escape properly.

Fuel pressure regulator Valve

Fuel injector malfunction or clogged injector:

try running some fuel injector cleaner through the engine or if the injector is really bad soak it for a bit in injector cleaner. To read more about injector malfunction click here.

Throttle position sensor malfunction:

this is not that common and I would recommend not mucking about with the sensor unless you've exhausted all other possibilities. Better to swap out the sensor to eliminate it as a cause then mess with it and maybe make things worse. If you really want to give ajusting the sensor a try I seriously recomend getting a good manual like a Chilton.

 

O2 (Oxygen) Sensor:

If the O2 sensor malfunctions it can send bad information to the ECM (Engine Control Module) which can cause the engine to run quite poorly

 

Timing is off:

I've heard guys saying this can cause hesitation and that's why I'm putting it in , kind of just in case. Personally I've never come across a truck were timing is the hesitation problem usually because if the timing is off ... to be frank the truck runs like total crap and it's obvious that the timing is mucked up so saying it was hesitating would be a grand understatement , but you never know.

Clogged or disconnected vacuum line: you can find a diagram of the engines vacuum system on a sticker on the underside of the hood, trace your line make sure everything is hooked up properly and check for kinks, pinches and clogs.

Fouled spark plugs

Moisture in the ignition system: When it's hesitating get a good electrical spray for disbursing moisture ( some people use WD40 but I've been told it can be bad for the wiring). Spray down the coil , coil wire and spark plug wires and the distributor. If the hesitation stops your issues is moisture in the system. Get new plug/coil wires , get a new cap and seal it with a little ultra blue. If the problem persists you might need to replace your coil or look elsewhere in the wiring involved in the ignition system.

Main fuse block:

the main fuse block wires are notorious for rotting , if your wires are starting to go they may just be lose and can some times on the off chance cause power surges that can cause hesitation... i.e. if the hesitation happens more on bumpy roads check your fuse block. For more information on what to look for checking the fuse block click here.

 

Hole in the manifold:

Not a real common one but if you had a big enough hole or crack develop in the manifold it could cause some hesitation.

Sticky throttle cable

PCV Valve (Positive crank ventilation valve) malfunction

Clogged EGR valve

ECM ( Engine Control Module)
For more information about the ECM and it's temperamental nature click here