I have this vibrating noise on my 96 civic that seems to come from right under the shifter. I removed all the interior pieces and lifted the round rubber seal that blocks out noise. It looks to be completely random but rarely happens in 5th gear. It happens both after shifts or just cruising in any gear(mostly 3 and 4). It sounds like two metal plates touching or vibrating. What parts are directly below the shifter?

 

the exhaust piping, if you got aftermarket exhaust piping, make sure the shifter isnt hitting it when you shift into the gears

 

As stated above, it is probably your exhaust.

The bottom of the shifter connects to the shift linkage. And the shift linkage is probably touching the exhaust. Do you have a bigger exhaust than OEM? Do you have a different shifter than OEM?

 

It's a second hand car and it came with a short shifter, I believe the exhaust is oem though. I am attempting to remove as many squeaks, pops, rattles and noises I have

 

take off the center console, the rubber boot surrounding the shifter, and throw the shifter in 5th, see if its touching the exhaust, or is dangerously close to it

 

it doesn't make any noise in 5th gear though. But I tried all gears, it doesn't touch the exhaust from what I can see and hear.

Maybe something is loose or not tightened all the way on the linkage? I was getting some new tires mounted and I asked if they knew about the noise. I previously had ALOT of play with the stick in gear and it was very loose. The shop tightened a bolt and the stick became a lot more firm. It wasn't fully tightened because it needs to have some play said the shop. Could this be a culprit?

 

It should have been tightened all the way. The bushing deals with the little bit of play that it should have. That's why bushings are made of rubber and not metal.

 

Check your engine mounts as well you could be getting movement when you change gears giving you the noise after shifting but it really sounds like exhaust and shifter noise.

 

Could also be a loose heatshield around the catalytic converter.

 

its your shifter. loose nut, washer, bearings or bushing.

i had a cheap short shifter before and had the same rattle.

 

I had the same thing happen to me. And come to find out three pieces from the shift lever assembly were missing. I'm not sure what piece or pieces you are missing but, look at the pic below and compare it to what you have on your car. More than likely you are missing some parts. I was missing part #6, 7 and 10 on illustration ( part#54109-SA7-000, 54110-SH3-003, 54115-SH3-000 ). When I installed them the vibrating sound finally stopped. And don't worry all ek's have the same shifting assembly, so the pic is a perfect reference. You could also go to HondaPartsDeals.com for more info..