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I've got a 2003 EX with the towing package. Was my parents' car for the last 17 years but recently they sold it to me. Car was bought new and driven by my dad most of its life. He never drives aggressively, and his commute to work is only about 5-7 minutes. Car now has 235,000 miles. Now that I'm driving it daily, I've noticed a fore-and-aft shaking in what feels like part of the drivetrain when the car is in 5th gear anywhere from 45 to about 60mph. The rhythm of the shaking feels as if it's matched to the revolutions of the engine. I thought for a few weeks that it may be bad engine/trans mounts, but I did the check on those where you shift the car from reverse to neutral to drive with the parking brake on and watch for engine movement; didn't seem to be a problem.

My dad has fairly complete service records from his ownership of the car, but I haven't been able to get a good look at those yet. I'm wondering if this is a transmission problem or something else. Believe the car has had this symptom for several thousand miles, but my dad refuses to admit he noticed anything wrong. I've also heard the tell tale sign of what I believe to be a front wheel bearing (or two) going out. Could a bad wheel hub or bearing cause a jerking/shaking like I'm describing? Car seems fine at any speed in all four other gears. But it also has a fairly regular, and more aggressive shaking when braking.
 

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The rhythm of the shaking feels as if it's matched to the revolutions of the engine.

Could a bad wheel hub or bearing cause a jerking/shaking like I'm describing?

Car seems fine at any speed in all four other gears.

But it also has a fairly regular, and more aggressive shaking when braking.
Taking these one at a time....

It seems that the symptoms you describe must be either engine, transmission, or drivetrain. If a wheel bearing was bad enough to do this, it would be obviously squealing and probably smoking after a few miles. I think the answer to the bearing question is "no way".

Since its fine in four other gears, the first suspect has got to be the transmission. Backyard Pilot Mechanic best practices indicate a 3x drain / fill of ATF (search for specifics if that's not clear) and sacrificing a goat while you pray that you don't need a new transmission. Since the other 4 gears work fine, the 5th-gear lockup is the prime suspect and it would still be worth a trip to a transmission shop if an ATF refresh doesn't work.

Shaking while braking is a separate problem, but address the transmission first. There's no point putting brakes in a car that has big potential problems.

Assuming the transmission can be revived, you should still expect a rolling-rebuild project with a car of this age. I think that I'm safe in predicting that most folks on this forum will advise strongly that you use this resource to learn more about your Pilot and how to work on it yourself. An "inexpensive" older Pilot will cost a lot of money if you have to pay someone to sort it out for you.
 

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Good info provided above for potential causes of the shudder/trans issues. In addition the trans pressure switches have been an known issue. Based on the age and mileage check to see if the radiator has been replaced in the past. Brake issues are probably related to worn warped rotors that can be replaced. Several maintenance items should be addressed to help keep this old Pilot on the road.
 

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When was the last time the tires were balanced? Granted you said the issue only occurs in 5th gear, so I imagine you’ve shifted to third gear while going at the speed where the issue occurs. If this is the case then probably not a tire balance issue.

As mentioned above 3x drain and fill to the tranny fluid is the first relatively cheap item to rule out.

Your year Pilot also has an externally accessible transmission filter. You might consider changing that out after the third drain and fill.
 
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