I have a 99 4 runner with the 4 cyl engine. A few mornings ago I started it up and it was suddenly running very rough. It sputters and spits and backfires upon acceleration. When I rev the engine up to around 2500 rpm it smooths out considerably. I can drive it ok when the revs are up and its under no heavy pull. However, going up hills it sputters under acceleration.

It had shown none of these symptoms prior. However....and I think may have caused it...I ran it really low on gas the day before it started running rough, probably nearly running it out of gas.

I went to NAPA and the guy sold me a bottle of fuel treatment...it did nothing. He seems to think it might be the fuel filter.

Any suggestions...other than to tell me not to run my vehicle so low on fuel. Thanks!

Should I have posted this is the forum for problems? Don't want to clutter up the wrong forum.

This is the place. It's your truck throwing a check engine light? Take it to Auto Zone and they will pull the codes for free.

I did...but the guy said he couldn't get codes for a 1999 model. Maybe I should try another Auto Zone?

The check engine light is flashing, yes.

Definitely go somewhere else and check the CEL codes. Pretty much everything switched to OBD2 in 1996. Whoever told you they couldn't pull codes on your truck had no idea what they were talking about. your symptom could be a lot of things.. update when you find out the codes.
My guess is you're having a misfire on one of your cylinders.

Or just didn't want to do it. I'm at AutoZone pretty often... always the same group of people working there. I've had codes pulled from my '00 several times there. My father in law went there recently and was told they couldn't pull codes from his '02 F-150.

You shouldn't be driving it with the light flashing. It can cause major damage to the catalyst system.

I just had very similar symptoms on my runner. There was a misfire on cylinder 6 (I have the 3.4 v6). In my research I found it could be either the plugs and wires, a coil pack, or a bad injector.

I started with replacing the plugs and wires but it was still running rough and there was still a misfire on cylinder 6. So next I moved the coil pack connected to cylinder 6 to a different cylinder reset the CEL. WHen the CEL came back I went to autozone to check the code. Now it was cylinder 4 misfiring so I knew it was a bad coil pack. Replaced the bad coil pack and now its running good as new.

My advice would be first to get your code checked like everyone else has said. Then you will know more about what you are dealing with and we will be able to help you some more.