Rough cold start

Dealer with vin and proof of ownership

No,low fuel isn't your problem. If there's enough fuel for the fuel pump to pick up your car should run okay. You haven't ruined anything. It's not your fault.

It is possible that a low fuel level - very low indeed - has allowed debris/dirt into the system and is causing a blockage. However, I think this is quite unlikely to be the problem you have.

You say the car idles rough - does it drive at speed okay? If it drives okay at speed you can rule out most fuel problems .. most.

Backtrack a bit .. has your car ever ran/idled roughly before? Cold weather can exacerbate a problem.

It could be the cold weather- fuel and injections system have cold start devices or sensors of one sort or another. It may be a faulty sensor. Get somebody to do a diagnostic check for you

I recommend replacing the fuel pump. I once experienced a similar situation with an Audi Quattro that was sensitive to temperature and would stop running when it was warm.

If you go to any Ford dealer with a picture ID, and ownership proof (Title), they can cut a duplicate key for your car. A simple one, without a chip on it, will cost you as low as $10. With this key you can unlock the door and get in your car. But there is a small problem. Your car key might have a chip on it.
For the 1999 model year, all Ford Motor Company vehicles equipped with the passive anti theft system will be using the PATS II system. The PATS II system was introduced on roughly half of the PATS equipped vehicles for the 1998 model year. The other half of the PATS equipped vehicles for the 1998 model year were equipped with the PATS I system. Many 2000 and later Ford Vehicles Use the E-PATS system, which uses an encrypted transponder in the key.
The Ford dealer will explain you if you need a simple $10 key, or a chipped one $50 key. If your key has a chip, then you have to reprogram it. Normally the dealer will provide you a written instruction how to do it.

Do you know if they have checked the catalytic conerter? It maybe that it is starting to plug up. they should be able to do a back-pressure test to rule this out or confirm. good luck!

It's flooded like you say.
If it's really flooded, you'll have to remove plugs and dry them off.
Install them.
Now when you crank engine, hold gas pedal to floor.
That will stop gas from spraying into engine.
You need to get the gas out of the engine for it to start.
Crank for 20-30 seconds with pedal to floor. Do this 3 times waiting 2-3 minutes inbetween cranks.
The starter needs to cool down.
Then after that start normally and see if it will start.
Remember if it will not start after 2 attempts, then the possiblity of it flooding is there and you'll have to clear out the gas by holding the pedal to the floor again.

I have a 2009 Accord 4 cyl. with 10,000 miles. I am having difficulty starting the car occasionally. Dealer said there is nothing wrong with the car.

If you like go ahead and let someone sell and replace your transmission but here is my suggestion! Check around and see if you can find a minor vacuum leak! This can simply be the big round hose that goes from the fuel injection to the power brake hub! This is normally a push in connector which has about a 1/2 inch hose clamped on it! If there is any kink or the connector is not in correctly a leak will occur and the transmission will shift rough as though you will be thrown out of the vehicle! Try unplugging this connector and plug it back in hard and straight and maybe you will be lucky and fix your problem. If the vacuum is correct your transmission will shift better than you have ever experienced!

probably a bit late to reply, but i had exactly same problem and now my engine has seized up, so please get it checked out immediately by Audi service center.