Hey, Atesh sorry to hear your woes.
Did you replace your rotors? I believe that could be causing you vibration. I had the same vibrating problem on my 323ci replacing the rotors fixed it. Though it did kill one of my inner tie rod joints. Make sure you replace those as well.
I'm pretty sure warped rotors can shake balljoints to death, and I wouldn't be surprised if that is where your clunking is coming from too.
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Zsp, Slicktop, Manual seats, 5spd