Civic 2000 Dilemma (D16/PK6 Variant)

I bought a Civic 2000 VTi Oriel AT about a year back. The guy sold it to me with a busted engine so long story short I had to get it overhauled.

Now after the overhauling, its not been able to perform completely normal condition, or maybe I'm being a perfectionist.

There are a few things I have not been able to get under control despite putting a lot of money into the car. It could be because I'm not diagnosing the problem right or due to my mechanic's incompetence. I've taken second opinions in the matter but to no avail. Anyways I'm citing down the problems below and hope somebody's able to help me.

1. After the overhaul, I've not been able to get it run on CNG with complete satisfaction. The RPM is always way too low at idle, around 500-700 RPM (temp at normal level) with the AC on. If I turn off the AC the RPM improves a bit by 100 RPMs. If I'm at a traffic signal with the car in still "D", the RPM drops wayy below to like 200-300 RPMS. Now I understand that at this moment the Transmission, the airconditioner, the brake master cylinders are all putting a substantial amount of load on the engine but I've driven other auto cars and none of them behave like this. Heck it never used to behave like this even before I got the overhaul. Now I've been to several CNG people, they've been able to fix this problem temporarily but it always returns after a few days.
I have a sort of a feeling that during the overhaul process, some settings of the EFi have been distrubed which arent normally disturbed during CNG installation and because of this its behaving like this. So, can this be one of the reasons? If so what do I need to check.

2. Secondly, the car's performance on petrol alot better as compared to CNG, but there is one thing that has bothered me. Sometimes the car's RPM goes up and down, from like 1000-1500 RPM. It does this two or three times and then settles down. Sometimes an anomaly occurs and it just stays up at 1500 RPMs.

On CNG, the RPM doesnt do the up and down dance, but sometimes it goes to 1500 RPMs, stays there for a few seconds and the check light comes on. Now at this moment if I put my car into "D", the RPM drops to 500 RPM mark. If I switch off my car and start it again, it returns to normal.


Personally I'm really baffled by these bizzare occurance of events. I possess some technical knowledge and am an engineer by profession, but so far I've not been able to sort out a solution.

Please help me. I've spent alot of money on this car uptil now, and have yet to see a return.

Thanks.