I have checked all the plugs and they are fairly new (Most likely replaced this year). The wires look fine, but I'm not sure how to test the ignition coils. It seems to me that one or more coils are not firing correctly. Anyone know how to test these? Also, when it starts to misfire at normal cruising speed, I'll step on the gas pedal a little and it helps to smooth it out. Taking the car out of overdrive sometimes helps a bit, (probably by increasing the rpms), but not always. Usually stepping on the gas pedal is the only way to smooth out.
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Re: Vehicle misses pretty bad, especially under load.
Try using a friction modifier in your trans fluid. I know this sounds crazy but I have done this before for people who come into my shop complaining that at 40-45 mph the car shakes or chuggs. I tell them to do a complete trans fluid change with our T-Tech trans machine and put in the friction modifier and it has worked any of times. You can get the friction modifier from Ford for about $10. As far as checking spark the only way to do this is with a spark checker while running.
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The vehicle is nearly 16 years old now, so it is quite likely overdue for a major tune-up (including plugs, wires, and coil packs).
Beyond that, verify adequate pressure at the fuel rail, and replace the fuel pressure regulator and/or fuel pump as required. If fuel pressure is adequate at all load ranges, suspect fuel contamination (especially if you have been using ethanol blend fuels over the past few years). Replace all fuel in the vehicle with fresh in this case, and that should solve your problem.
It should go without saying that it is not possible to provide a diagnosis of your issue without knowing the YEAR, MAKE, and MODEL of your vehicle.
That being said, misfiring under load is most likely a fuel problem, maybe something as simple as an old, clogged fuel filter, or contaminated fuel (especially if you've got an older vehicle and are using ethanol blend fuels).
Check to make sure the EGR valve is not opening prematurely. It is is the controller could be bad or the valve could be gummed up with carbon. Also check the ignition wires (spark plug wires) to see if they need replacing, they may be "leaking" under a load.
Firing order okay? the MAF can do this to you (Mass air flow) a bad connection at the distributor can do this. The distributor connection can do this if the 180 signal is missing going to the ECM. So wiggle test that connection and inspect that male to female connection. The MAF (mass air flow) in this particular year it was called a volume air flow sensor so if this signal is missing signal to the ECM it stumbles the vehicle so wiggle test that connection also check fuseable links and ground for this mass air flow.Rule of thumb a backfire always occur when timing is off giving a lean mixture. and a miss under load is a meaning for not enough fuel.
Had a similar problem, cannot explain it but dealer stated that we needed a new software update in the computer of the car. Once they did this the transmission shifted better and did not miss in high gear. I don't understand why this fixed it when we did not have a problem with it before, you would think that with this type of fix this issue would have happened when first purchased not 2 years later.
Factory plugs are not always the best tool for the application. In your case, you use the vehicle for something that would be deemed as heavier usage as per your question. What you need is to contact your local dealer or Auto parts store for platinum tip or double platinum tip plugs for a greater spark, o r you could replace with the recommended pluga and regap them for a greater spark...