let me answer this, engine check light turns on because oxygen sensor on this vehicle is not connected with cng emulator/advancer by default so if get this connected then this problem will be resolved.
if you have an OBD tool something like eml327 and you look into the values of (STFT) short term fuel trim and LTFT long term fuel trim then you will realize that STFT value starts to increase once on CNG and within a minutes and earlier it hits -25 % and that is once, it cannot exceed further and engine check light turns on which indicates an issue with oxygen sensor or oxygen sensor malfunction.
now, once running on petrol, again cross verify the STFT as it should remain within -3% to +3 % while idling and should never exceed +-10%. that is how you know as problem with car average on petrol.
as far as idle rpm is concerned, you need throttle body cleaning. if you dont have time and looking for a temporary solution then spray wd40 and carburetor cleaner inside throttle body and give it a good clean from outside by pulling the throttle plate etc. if too much dirty then better get it removed and have it serviced.
last advice, entire air filter assembly sits on opening of throttle body. their is a small screw which tightens the grip of filter assembly on opening of throttle body. make sure that its tight enough and engine is not sucking air from gap inbetween.
P.S: get the oil drained from CNG kit, that is also one cause that your starting the vehicle in morning fails on cng.
P.S: after throttle body cleaning, if problem remains intact on cng only then try to adjust the idle control knob on cng kit.