What is going on? Sometimes when im sitting at a light and go to put it in to first the shifter will only go in about half way or so. So what i have to do is shift into second then back into first to get the gear box into first gear... What can that be?

 

Mine does this sometimes too - my guess is the synchros are wearing out. Here's something you can try if you have fine clutch control: actively try putting it into first, but use only the normal amount of effort. Bring the clutch pedal near the engagement point, and slowly release it. Once the clutch hits the engagement point the shifter should pretty much pop into first gear. And when this happens press the clutch in to make sure you don't grind gears or anything like that.

 

Synchs aren't lining up just right - happens in a lot of cars. A high-quality synthetic fluid may help if it really bugs you but it's really not anything to sweat.

 

Another thing is from first to second even sometimes 3rd when I'm shifting I hear a clink noise as I'm taking my foot off of the clutch. Any idea of what that can be?

 

I did a fluid change on my trans with Redline 75W90 about 8000 miles ago, didn't make any difference for me.

Is your car Quattro? If I recall correctly the rear diff carrier or bushings or something like that could be worn out and cause this sort of thing.