If you hear an odd noise coming from your 5-speed transmission, this post is for you.
There are 2 common things that happen to the 5 speed transmissions in our generation Honda.
The first of which is somewhat common. This is the throwout bearing.

This is how to diagnose it.....
-Start your car.
-Roll up the windows, turn the radio off, and turn the blower motor for the AC/heater off.
-put the car into neutral, and press in the clutch
---- if you hear the noise now, it is the THROWOUT BEARING. If you release the clutch, the noise should go away
The reason it makes the noise like this is because when you have your foot off the clutch, the throwout bearing is not spinning, and it has no force on it. But when you push the clutch in, the throwout bearing forces the fingers on the pressure plate in, causing the clutch to release. The bearing is spinning however fast the motor is turning at this time. So if the bearing is bad, it will make noise.
This is a rather simple fix for a shop to do. They have to take the transmission out, and replace the throwout bearing, the replace the tranny. It is basically the same work as replacing a clutch.
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Now, the second (and seems to be more common) problem is the input shaft bearing.
This is how to diagnose it.....
-Start your car.
-Roll up the windows, turn the radio off, and turn the blower motor for the AC/heater off.
-put the car into neutral, and take your foot off the clutch pedal
---- if you hear the noise now, it is the INPUT SHAFT BEARING. if you press in the clutch, the noise should go away.
The reason for this is because when you have the clutch engaged (foot off the pedal) the motor is spinning the input shaft on the transmission (even when in neutral). The bearing has a plastic cage inside of it that holds the small ball-bearings equidistant apart. This plastic cage can be broken by even a completely stock car, if it is driven hard (shifting hard, running sticky tires, etc). When this plastic cage breaks, the ball bearings load up one side of the bearing. This allows the input shaft to walk side to side slightly, which causes the gears to not mesh up right. This causes a whining and growling sound. But when you press in the clutch, the input shaft stops spinning, so the noise goes away.
The way to fix this is a lot more difficult. You have to completely remove the transmission from the car. Then you take the shifter assembly out of the tranny, remove the speed sensor. Then you have the split the case apart. Next you have to remove the differential and the Spider gears. Now you will have access to the bearing. The bearing is $23 from your local honda dealership. Once you install it, put the tranny back together and slap it in the car.
I hope this helps you guys out. A LOT OF SHOPS MIS-DIAGNOSE THE INPUT SHAFT BEARING FOR A THROWOUT BEARING!! This means that you pay for them to replace the throwout bearing, then when you drive it home and its making the same noise, you take it back and pay them to fix the input shaft bearing.
I am trying to help save you guys some hard earned money with this. Diagnose this yourself. Print out this guide, and take it into your tranny shop. Let them diagnose it with the help of this guide. And hopefully you will save some cash in the end AND look like you know what your doing.
