Unfortunately any knocking noise is a bad thing.
The only things that can happen when the cable is too loose is that it will not want to go into gear. If it is to tight it will not disengage and the clutch will slip as if you were pressing the pedal.
I had a 1990 Integra and they are pretty tough cars. But, if you have a knocking noise that only occurs when in gear, it is probably a bad bearing on the input shaft. That includes the throwout bearing. But that would make constant noise. Either way the transmission will more than likely need to be looked at.
Just to let you know the best way ti adjust the cable for the future.
On the transmision in the front you will find the clutch arm at the end of the clutch cable.
There is a plastic adjusting nut on it.
Tighten it untill you can only move the clutch arm a little bit by hand.
I found it hard to adjust by pedal travel. Adjusting it at the arm will ensure that it is disengaging the clutch as much as possible without risking it slipping and damaging the clutch.
If you look on Craigslist or EBay, you can probably find a used transmission.
Re-builds can be expensive as the bearings and seals are not cheap.
Have a mechanic listen to the knocking noise because there is the possiblity it could be a broken motor mount or soemthing that knocks around under load. It is kind of unusual to have damage even at that mileage unless the oil was low or never changed.
If you look online for a transmission, look for a JDM.
This stands for Japanese Domestic Market. There are laws in Japan that require a new engine at 30K and this means there are motors and trannys to be had with 30K on them for reasonable prices and shipped as well.
I hope this helps you out.
Tuesday, September 6th, 2011 AT 1:01 AM