I had a same problem with my 3y-PU toyota engine installed in Kia Sportage. It took me long to find the problem and I would love to share my experience, It might give you some clue.
Same problem as you described and I was facing high fuel consumptions. Mechanics checked spark plugs, plug wires, distributor, throttle body all cleaned up, IAC and MAF sensoor got checked, EGR Valves checked, PCV valve checked but problem still not gone. Mechanic told me to get valve clearance job done, but I was not in agreement with him to do valve adjustment as car was starting in morning by just touching the self starter.
I then inspected whole vacuum system and found the leak in the vacuum hose going into the valve cover (black thing on engine head), this is the vacuum hose not mounted on PCV valve, the clip was broken and it was causing a vacuum leak. I just put new clip on that hose.
In my case there was another problem (which I guess you might not have). The CNG fuel supply pipe was put into the Air Intake pipe (to the point where clean air is coming after the air being filtered). That was done by extreme jugaad and epoxi maagic was used to seal the junction (done by some mechanic previously before I purchased the car). I found the leak in that hose too and managed to fixed it.
After all these fixes, no rough idle, ideal fuel consumption (jumped from 180 to 230 in one filling).
It might help you guys. All the best with your car fix.
