99 clk320 rough ide in drive when its cold?

[VegasCLK]

99 clk320 with 119k miles. I did most of my service and maintence since it had 30k miles The car shakes and idle rough when the car is in drive with the brakes press. The idle problem goes away when the engine reachs normal operating temperature. The problem recently started and I need to know what needs to be fix. Also sometime the engine makes tapping or clicking noise when the engine is cold. The noise goes away when it reachs normal temperature or when the rpm is above 2k.