Dear brother!
The clutch box noise you mentioned is a manufacturing defect of Honda CG125 Euro2 model. It'll be fixed and replaced under warranty FREE OF COST. Half of your problems are because of it...
And vibrations?
Well, Euro2 model has very less vibrations as compared to previous models but you can get your bike's all NUT/BOLTS/SCREWS tightened from mechanic including the axle...
Hope that'll help getting rid of your problems
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