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I can help you break a couple of things down here; as for the repair, it's really up to your tools and skill set. If you have a transmission noise when you let the clutch pedal out with the engine running, this is often the input shaft bearing. If you have a grinding noise when shifting into a particular gear, it's likely you have a synchronizer problem. If you have a grinding noise when shifting into every gear, check your clutch and clutch adjustment. If there are other grinding or whining noises during transmission operation, you might consider changing the transmission fluid and rechecking for the noise. You'd be amazed at how well this can work sometimes.

It is very important that you use the correct fluid when changing manual transmission fluid. Unlike automatic transmission fluid, which is pretty much universal, manual transmissions are anything but. I've seen everything from gear oil to automatic transmission fluid in manual transmissions. It just depends on how it's designed. You must consult the service manual to find out which transmission fluid is best for your vehicle. In the case of Hondas, it's Honda MTF. You can also use GM Syncromesh fluid. I've had great success curing manual transmission issues in some Honda transmissions with Syncromesh fluid. I do not recommend using regular motor oil in a Honda transmission.

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In summary, try to find out if the noise is coming from the transmission or the clutch. If you have a clutch noise inside the bell housing, don't waste your time. Get a new clutch, pressure plate, throw out bearing, and pilot bearing before you pull the transmission out. You're going to have it out anyway; you might as well be ready to replace the parts should you need to. As with automatic transmissions, if you hear a clunk or thump as you change gears, check the engine and transmission mounts. Loose or broken engine mounts can cause this type of noise. For more in-depth information on manual transmissions, see the Transmissions article.