Yaar there may be some reasons behind your gear box problem which can to be found step by step.
How is your gear oil condition and quantity?
Less gear oil means obvious grinding sound even in idling.
There are gear forks under the gear lever by which gear lever engage and disengage differnt gears.If gear lever or gear forks are having blunt edges there might be problem in shifting and missing gears resulting in sound.
Your pressure plate might have loosen the tension of its fingers which is not making your gear assembly idle when you press the clutch for shifting gears.
There might be some shaft ellignment troubble due to some bearings when your mechanic refitted the gear.
Regarding missing,if your car do missing on petrole only then might be fuel filter,fuel lines,fuel pump,nasty injectors,dirty fuel tank and most commen dirty fuel.
If your car do missing on cng aswell,there might be problem with your ignition system including plugs and wires.
Also get your car checked with obdII computer if there is some problem in air/fuel ratio or any sensor relating to this ratio is getting bad.