Why is my pickup running rough?

Changed plugs, wires, cap, rotor, and coil, also treated fuel tank and changed fuel filter 3 times to eliminate contamination but the vehicle is still running poorly.
My car has a manual transmission.
Experienced mechanics share their insights in answering this question :
Hey there. You should take a fuel sample in a clear glass container, and then if you put the container in a freezer, it will separate the water from the fuel and you will see if you have a lot of water in the fuel.

If there is water present, then you will need to remove the fuel water contamination. If there is no water and gas is not contaminated with anything then you will need to have the engine computer tested for running codes to see if the EGR valve is stuck open causing the rough running engine.

If the EGR is stuck open, it will cause a rough idle to mid throttle but run good at higher RPM’s. If the EGR is not stuck, then the fuel injectors would need to be checked for flow causing one or more cylinders to run too lean from previous fuel contamination. If this is the case, then you may need to remove and have the injectors cleaned or replace them with new ones. For a precise diagnosis, consider YourMechanic, as a certified technician can come to your home or office to inspect the rough running problem and follow through with repairs.

How to Identify and Fix Common car Problems ?

Our sources include academic articles, blog posts, and personal essays from experienced mechanics :

The most common reasons a Ford F-150 has rough idle are a vacuum leak, an issue with the spark plugs, or a problem with the ignition coil. Search our network of RepairPal Certified shops near you to speak with a technician about your issue.
Here are a few reasons a Ford F150 might shake at idle:

Spark plug issue. Vacuum leak. Ignition cell fault.

If the torque converter is broken, or if there is a low fluid level in the transmission, the converter will not do its job, and the car will be unable to maintain power at low speeds, which causes the engine to shut off. A defective TCS or torque converter solenoid can also cause this issue.
Faulty spark plugs and ignition coils are the most common reason for a running rough engine that causes shaking and a flashing check engine light. The shaking is usually from a misfire, and it`s common for the check engine light to flash for ignition-related codes.
How to fix it? Cleaning or replacing the fuel filter and adding a fuel injector cleaning treatment to the fuel tank should take care of clogged fuel injectors. If the rough idle persists, it`s time to take your car to an auto repair shop.
Engine Misfires

Perhaps the single most common cause of rough idle comes in the form of a misfiring engine. As you may know, any automotive engine contains multiple cylinders. Each of these cylinders contributes to powering your car by combusting a mixture of gasoline and air.

The Ignition System

The shaking occurs as your truck`s engine struggles to remain running while at idle. A few common causes within the ignition system are: Engine Misfires. Faulty Spark Plugs.

The most common cause of the shaking most often happens near your tires and rims. The tires and wheels connect your vehicle to the road, and if anything is a bit wonky, will notice. It may be something like a broken transmission or a broken control arm.
If an engine is not getting enough fuel (this is called “running lean”), due to fuel pressure (regulated by the fuel pump and regulator), restricted fuel injectors, a vacuum leak or really anything that throws off the fuel mixture going in to the engine, this can cause the surge.
The Ignition System

The shaking occurs as your truck`s engine struggles to remain running while at idle. A few common causes within the ignition system are: Engine Misfires. Faulty Spark Plugs.

Causes of a rough idle. Many different problems could result in a rough idle for your car or truck, including: dirty fuel injectors, clogged air filters, bad spark plugs, and a variety of exhaust system issues.

Relevant Questions and Answers :

the most relevant questions and answers related to your specific issue

01 mustang v6 running rough at idle and drive. Please help. Replaced a bunch, still can’t figure out issue.
ANSWER : This may be a sign of a faulty MAP sensor as the vehicle responds adversely to a load put on the motor (i.e. putting it in gear, turning on AC or engaging the brakes). The Manifold Absolute Pressure (MAP) sensor senses engine load and generates a signal that is proportional to the amount of vacuum in the intake manifold. The engine computer then uses this information to adjust ignition timing and fuel enrichment. When the engine is working hard, intake vacuum drops as the throttle opens wide. The engine takes in more air, which requires more fuel to keep the air/fuel ratio in balance. When the computer reads a heavy load signal from the MAP sensor, it adjusts the fuel mixture to slightly more rich than normal so the engine can produce more power. The computer will then retard (back off) ignition timing slightly to prevent detonation that can damage the engine and decrease performance. This may also be caused by other closely related components such as a dirty or failing mass air-flow sensor, a faulty throttle position sensor or potentially a vacuum leak. I would recommend having an expert from YourMechanic come to your location to diagnose and inspect your vehicle.

Vehicle started running rough while driving. Now running/idling rough running rich.
ANSWER : Hello. From the symptoms you describe, it would appear that your vehicle is having issues with the oxygen sensors. P0172 is the code for bank 1 being too rich. This can be caused by a wide variety of issues. The other two codes are for the sensors on bank 2, having excessively high voltage.

This may be due to the rich condition, faulty oxygen sensors, or faulty wiring. The black smoke and soot is a result of excessive fuel that is not being properly burned, and exiting the tailpipe as smoke. A few common causes for these symptoms are a bad fuel pump, fuel pressure regulator, or engine management sensor. As engine management systems can sometimes be difficult to diagnose, I would recommend having the rough idling issue inspected by a professional technician.

The truck intermittently, has a very rough idle, and runs rough,usually after warming up.
ANSWER : Hello. This can be caused by a number of different things. If this occurred right after you had gotten fuel then I would start by testing the fuel pressure. I would do this when the vehicle starts running poorly. It is possible that the bad fuel contaminated the fuel pump and it is not putting out the right pressure. If the fuel pressure is fine then I would check the other sensors readings with a scan tool. One other common thing that I have seen on this engine is a leaking intake manifold gasket. It starts leaking on the bottom side and that leak causes the MAF and MAP to not read correctly which causes it to run like this. If you would like to have this rough running condition looked at, consider having a YourMechanic certified techniciancan come to your home or office to diagnose why it is running rough.

replaced bad coil pack and new coil not sparking car starts but runs rough engine light on blinks sometimes
ANSWER : Hello and thank you for your questions. If your engine was rebuilt about 10 months ago, the question is to determine if the management system has been installed as well. With the symptoms that you are having, it sounds like the coil packs are old and in need of replace. You replaced numbers 1 and 4 and now number 6 is not firing. I recommend replacing number 6, 2, 3, and 5. This will ensure that you have all 6 coil packs that are new.

Just because the coil packs are okay during a test doesn’t mean that they are functioning correctly. Coil packs on Buick vehicles from 1998 – 2005 last between 150,000 to 200,000 miles. I also recommend having your fuel injection system flushed. Unless you have new injectors, the old injectors could cause a cylinder to fail, even though it is working correctly. These symptoms can cause the engine to have a rough idle and rough running during conditions. If you need assistance troubleshooting the rough running condition, I recommend having a professional, like one from YourMechanic, inspect the car and move forward with repairs.

Car is running roughly at around 45 mph
ANSWER : Hello. It is possible that all of the spark plugs and spark plug wires need to be replaced in order to fix the problem on your Plymouth Grand Voyager. Also, if carbon has built up in your intake, throttle body, and EGR valve parts, this may cause the problem you are experiencing. Having the throttle body cleaned as and a fuel induction service may help as well. Have a certified technician, such as one from YourMechanic, come and assist you with diagnosis and repair of your car’s rough running at high speeds.

Cranks and runs rough have to keep foot in gas to keep running. Has new fuel pump and died while driving after pump was changed
ANSWER : Check fuel pressure. There are only three possible explanations: a fault in fuel supply (plugged filter, injectors, etc.); ignition system problems; and air induction including the idle air control valve, throttle position sensor, mass air flow sensor and vacuum leaks including the PCV and EGR systems. If obvious, and easy to check, possibilities do not reveal the fault, the recommended service to request is a rough running diagnostic and the responding certified mechanic will travel right to your location and get this diagnosed and resolved for you. It is also possible that diagnostic trouble codes have set and the mechanic will attempt to retrieve those using an appropriate scan tool. If you have further questions or concerns, do not hesitate to re-contact YourMechanic.

Pickup is running rough, jerking, stalling, and not idling over 3000 rpms
ANSWER : Hey there. This sounds like an air/fuel delivery problem which may be a result of a dirty or failing mass air flow sensor. This may also be a result of a failing O2 sensor which may also cause an incorrect adjustment to the air/fuel ratio causing the cutting out and over or under fueling the motor. This can also happen when the mass air flow sensor is not properly reading the air flow which causes an incorrect fuel adjustment to be made resulting in the same type of symptom. I would suggest having an expert, like one YourMechanic, come to your location to inspect the rough running issue and determine what may be causing this.

Car runs rough until warm, and then runs fine.
ANSWER : I would have a technician inspect your rough idle. He will probably also check for codes on the computer. It may be the air temperature sensor malfunctioning if it idles rough only when it’s cold. You may be able to remove it and clean it or replace it. If that doesn’t fix it, it may need to be checked out by a technician.