Had exact same problem - mine was making really annoying noises in 2nd and 5th. There is a tension spring inside the gear shift knob that holds it in place. Even though it is under tension, certain vribrations make the thing produce some really annoying noises. My solution was to take the gear shift knob off, remove the spring, squirt some silicon caulking into the shift knob, put spring back in and re-attach shift knob. Once the caulking sets up, it acts like a little rubber damper and complety stops the spring from vibrating. Try it, you will be surprised how much more quiet it is.
Edit: also, if it's shifting really ruff, take it in and have it checked. The Libby is no race car, but mine shifts pretty darned smoothly if you dont rush it when shifting gears. The manual trans in the Libby does not like to be rushed
