1998 Honda civic dx jerks while driving?

I recently bought a 1998 Honda Civic DX 5 speed. When I get to around 3-4 thousand rpm ( guessing the car doesn't have a rpm gauge ) the car starts to like shake and jerk. Also when I'm in neutral and let out on the clutch it makes a grinding like noise. Where I bought it told me it was a throw out bearing but me and my friend replaced it and it's still making the noise

Lemon! Heads, Trans, Plugs exc.

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