Hello. I have a 1997 Honda Civic EX Coupe with a 5-speed manual transmission with 255,000 miles on it. I bought the car cheap knowing it had this weird grinding noise. The noise only occurs when accelerating harshly or engine braking, which leads me to believe it has something to do with backwards or forwards resistance, as no noise can be heard when the transmission isn't engaged with the engine (when I release the clutch or put the car in neutral it don't make any noise.) I have a video of me recreating the noise with the car jacked up on stands with the wheels off the ground. I give it gas and push the brakes a little, which causes backwards resistance which causes the grinding noise.
https://www.youtube.com/watch?v=WvI8...ature=youtu.be

 

I just had the transmission go bad on my 1997 5 speed civic. I tried some of the same tests as you did. Finally I drained the transmission oil, and saw that it was loaded with tiny metal flakes. It had about 250,000 miles on it. Always used Honda MT fluid.