edit: only makes kocking noise while the ac is ingaged and it's worse in drive at a complete stop than in nuetral at a complete stop. It's an a4

Ok first off sorry this is so long. I posted b4 but now i have just about all the info except a sound clip. I tried to get that but its hard to capture the sound. Anyways heres the info

I started the car about a month ago after letting it sit for 3 days. The car shook vilantly for about 3 minutes with a whistling sound then went back to idling fine with no problems. Well for the last month or so when I start up the car it makes this whistling noise, but only when i start it in the morning with a lot of moisture in the air. After I put it in drive the car stops and run fine. I feel no power loss or anything. All the guages read fine. The oil temps about 30. It idles in Neutral around 1k and drive around 700. When i am slowing down or at a complete stop in drive the car will make a knocking noise that fades in and out. It's not a constant knocking and its not very loud at all. Only does this when applying breaks, complete stop while in drive , or in reverse. Mainly low rpm type situations. I thought maybe it was the rip in my elbow so I replaced it but the knocking is still there. Can some one help me?