@zubairmanzar
its my real pleasure being of use for u.
i doubt you're air valve beneath the mixing chamber have got lots of carbon deposited on it. when i bought my vehicle, first thing i did was is to clean it with a carb cleaner spray (commonly known as NASA spray in karachi market). Does your car miss whenever are on lower gear and it changes gear, between 10-15-10-5 kmph speeds?
IMHO If you have got a clear air filter, cng tuned fine, acceleration/pickup is ok, then the only thing left which is causing vibration is carbon, unless some other serious fault.
if whatever i have said above doesn't make a sense to you, goto your mechanic and tell him that it has been suggested to clean it via above method and let me do the rest. its easy to do once you've learnt.
i know of 1 good cng shop at Alladin Park, named SHAH CNG... they have a few mechanics and I believe the best one is named Waqas, so ask for him (fyi i checked with the cng shop with a friend today and Waqas on a few days' holiday)
Hope this helps.