1990 Z24 problems

[93_grand_gt]

Hey hows it goin
I have a 1990 Z24 with and automotic i have been having some issues so i was hoping some one had some ideas
Ive been gettin alot of water leaking in and leaving a puddle on the passenger side floor, ive noticed that there has been some water dripping from the sunroof. could that be causing myproblem??
Also i have a clunking in the front end driver's side i think. I have all new struts and shocks put in plus a new ball joint and axle on the driver's side but the clunk is still there and it also tends to wanna squeak when it is cold in the morning.
there is one other thing when the car is idling in park or in neutral it feels rough sitting inside the car like its not running smooth but it is, its kind of a hard thing to explain.
If anyone can help me with either one of these problems that would be great
thanks alot