2002 Protege misfire

About once every three weeks when I come to a stop in my car it starts to hesitate severely. It appears to me that it is misfiring. I have replaced the spark plugs and ran my tank down to about empty before refilling to ensure no contamination in the tank. When it starts to misfire, if I shift it into neutral and rev the engine the problem goes away and won't occur again for another 3 weeks or so. I'm not sure where to go from here seeing as how it happens rarely and no warning lights go on. Any ideas on what I could check next?

does the vehicle only exhibit the misfire when coming to a stop or after driving and then slowing down?

if so, odds are your egr valve is hanging open. there was an issue with the vehicle in which the egr valve would rust along the shaft and it would thus stick open allowing exhaust gas to enter the combustion chamber at idle.

the way to determine if this is the case, primarily, is to identify when it happens. egr will never open fully at idle. it should only open at cruise speeds and steady throttle. if you are willing to do so a simple complain description at your local mazda dealer should lead them to test your egr stepper motor and monitor your baro sensor readings while doing so.

if the car only stumbles after some driving and while coming to a stop this is most likely your problem. while i have seen many many other similar problems with this car this may be your best guess... so... either drop the 90 bucks at your mazda dealer to have it diagnosed or throw the 200 dollar part at it. your call...

hope this helps a bit.
good luck.

You may want to try cleaning the idle control valve. It's mounted to the throttle body. They build up debris and stick causing the idle to surge or the car to hesitate then surge or die. The Protege has two problems with the idle system, the idle control valve and the EGR valve. The opening in the bottom of the intake manifold that leads to the egr valve builds up carbon and clogs up. You get an EGR excessive flow error. It's not very hard to dissassemble the throttle body to fix these problems, just use proper torque specs when you put it back together (around 18 ft lbf for the bolts, 21 ft lbf for the nuts) and use anti seizing on the nuts and bolts.

When I take off from idle I can hear something rattling around inside the bottom of my exhaust. I went under to car to see if something had come loose but couldn't find anything. I knocked on the bottom of the exhaust that drops down from the manifold and found where the noise was coming from. Could one of these possible problems be related to this?

It depends what is causing the noise. I would recommend that you take it to an exhaust shop. If it's your catalytic converter, it's a bit early in the cars life to be having such problems - check your warranty. If it's the O2 analyzer you should be getting a check engine light as well. I can't imagine what else could be a source of material that could be rattling around in the exhaust between the manifold and your muffler.

What would happen if I took the EGR out of the equation to see if that was the problem. If I took out the EGR and temporarily sealed off the port on the engine for it what could happen? Would it cause damage to the car, would it kill my gas mileage?

It seems the EGR valve was my problem. I removed the valve to inspect it and when I removed the solenoid that opens the valve I found that the valve itself was spring loaded. I pushed the valve open manually and there was so much carbon build up that it stuck open. As severe as it was I'm surprised I wasn't having the hesitation at idle more frequently. I purchased a new valve from my Mazda dealership and have had no issues since I replaced it.

what type of plugs if they are bosch try ngks and i would research sea foam treatments very helpful and may solve your problems since this will basically steam clean all of top internals in a sense it should aslo clean the egr all in one shot 1/3 into a vaccum line ( thicker one closet to the brake booster ) and 1/3 into your gas tank

Something to watch with the egr valve. The tube that leads to it comes off the bottom of the intake manifold and it tends to collect carbon. The trick is to remove the throttle body and the egr valve, then spray carb cleaner through the tube. This is also the solution to an EGR excessive flow engine warning light.