Bro as per my knowledge these could be the reasons:
i). Your tyre must be touching the sheet placed on top of tyres, it might have been unclipped 4rm sumwhere due to which it makes noise.
ii). If your car is CNG & as you quoted it's a bit high then most probably there are spacers installed at the rear springs, get rid of them & hopefully the bumps will reduce.
iii). Regarding axle tuk tuk, you might need to change the axle seal or the axle boots might get repairs.
iv). Cudn't guess the fourth one, so sorry abt that :-(.
Please note, you must take opinion from your mechanic first as they will tell you precisely abt the problems.
I'll recommend you to either go to Honda Pit stop @ Nazimabad, they are really good people & use only genuine quality parts. Though they are a bit expensive but I believe it's a lot better to spend a Rupee together rather than spending 25 paisa each time for 6-7 times. In the end you will lose!!! that's my experience.
If you are concerned abt the suspension, my recommendation to you is better go 2 Shah G, I've lifted my 99 civic a bit as it was lowered & he did a fine job. So I'll prefer them as they are quite professional & reasonably priced. You may go 2 any Shah jee axle wala it's almost in every part of Karachi.
Hope the above will be of any help to you.