Hello, I have a 2000 Protégé LX 1.6 - I have never had any problems with it, and it ran fine until recently when it started idling funny. Everything was fine while driving, but when you stopped the idle would drop low then come back up. I thought it was because the battery was going bad, but when I changed the battery it made it worst. I am not sure if it is a charging problem, sensor problem, or fuel system problem. Anyone had similar problems or heard of anything like this?

Also does anyone know where the fuel filter is located on this model?

 

Your plugs and air filter are ok? A check of the base idle speed would be a good first thing to check. One of the most common problems on this year with 1.6 engine was faulty Mass air flow sensors. Mazda has even extended the warranty on that part for 7 years or 70,000 miles as long as it is not a California emissions car. If none of these pan out then removing the Idle Air Control Valve to clean out might help as well.
Almost forgot. You do not have a replaceable fuel filter. The only filter is the pickup screen on the fuel pump inside the tank.