At first when you start the car it would make a whining sound and when you press the clutch in all the way it would make a whining noise. I kept driving and it stopped. Now it kinda jerks when i set it to gear and slowly engage into gear. Does the throwout bearing need replacing?

 

i have the same issue, i got a 2000 honda civic.

 

we replaced a throwout bearing, and it didnt change the noise

 

When you leave it in neutral without stepping on the clutch does it make noise? That's usually indicative of the input shaft bearing