Fuel Air Metering

Hello everybody:

I have a civic si 02 and has been giving me problems for about 2 months. The check engine light gives me different codes every time, but they all say (Manfacurer air fuel metering)
Last time I ran the scanner it gave me the following codes

P1259 Manfacurer air metering
P0171 System too lean Bank 1

When I stop on a red ligth it feels like the engine is about to stop, but then it revs up to 2000 rpm (by itself), and goes down again.
The exhaust throws very thin black dust and smells a lot like gas.
When I take my foot off the gas pedal the car shakes a little bit.
And the car is consuming a lot of gas lately.

It all started when I accidentally drove through a huge pond that formed in the road during a heavy rain, at first my cousing told me it could be that water just got into the intake but now I don't think is just that.

Any suggestions what it might be?
What should I check?

Thanks