ecu does not increase the idle speed, if that is choke on, idle will come down in few minutes.
they have either fiddled with tps.(throttle position sensor. or left a vacumm line disconnected and manifold air pressure is getting wrong readings. better would be you don't touch anything just disconnect battery negative terminal for few seconds and connect again if that don't fix anything, tell them to fix it.
if that cng setup in there than i don't understand anything about it.- spectra can guide you better about cng.