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Walnut Creek, CA
This can be caused by any number of things I'm afraid, from the mass air flow sensor to fuel injectors to vacuum leaks to a fuel pump. It really needs to be diagnosed. The technician will need to scan for any trouble codes and perform a proper diagnosis. It sounds like this is mainly a problem once your van is at operating temperature, and only bogs/stalls under load. All of that information can help a technician figure out what is going on with your van. Is it only accelerating from a stop? anytime you accelerate? What is the outside/ambient temperature? Does outside temp matter? Does it only happen when the engine is cold? only happen when the engine is at operating temperature? When it bogs, do you see any black smoke from the tail pipe? I'm sorry I can't tell you exactly what is going on with your van but I hope this will point you in the right direction.
First, (nearly) every Jeep will start to leak from the pinion seal (front or rear). Diff covers also. There is a chance the groaning could be your carrier bearings or axle/wheel bearings, or both. I am assuming the clunking you mention is from the rear of your Jeep, that may be your limited slip starting to go south too. It also may mean you need to change the fluid again and use the correct limited-slip additive. With Jeeps you have an amazing amount of options because of people modifying them for off-road or rock crawling. What you decide to do I think depends on your goals. If you're doing daily driving, stock tire sizes, the Dana 35 should be fine. If you've gone larger on your tires, and go off-road the Dana 44 is an option. The Dana 44 that came on some of the V8 Grand Cherokee's does not have a great reputation for strength because of the cast aluminum housing. I am more familiar with Toyota crawlers but sites like JeepsUnlimited and Pirate4x4 will have info on axle swaps so you can know what to look for used (use the search functions and read the FAQ before posting questions). That leads to the next option. With people swapping to Dana 44's and 60's, you will probably be able to find a stock 35 complete drum-to-drum. A lot of wrecking yards specialize in Jeep parts too. (http://www.jwjeep.com/ for example) I'm afraid I can't say what a rear-end rebuild will cost without knowing what exactly what you need. I would look into the price of a used, good axle, and then decide if it's worth rebuilding your original axle. If you feel like reading some tech, I have used this for my friend's Wrangler and my Toyota http://www.4x4wire.com/jeep/tech/
I'm not sure what the clunk may have been but you might check your idle speed motor and your throttle position sensor (TPS). Any vacuum leaks will cause a high idle condition as well. The Idle speed motor won't always set a Check Engine light unless it's electrically defective. If it's mechanically defective it won't set a code. Vacuum leaks won't always set a code either. If you're not familiar with these parts, I suggest taking your Jeep to a qualified technician to be diagnosed.
You should clean the floor around where it normally leaks first. The next time it leaks soak some up with a white paper towel or napkin. You should be able to identify if it is coolant or normal water. Coolant will have color (typically orange or green) and smell. You may also notice the coolant level dropping. If you're not comfortable working on your truck, it would be a good idea to take it to a good shop if you determine that it is, in fact, coolant. If it's normal water, it could be condensation off the AC compressor finding its way to the ground. Many vehicles activate the compressor with the "defrost" function.
Are you saying, after the engine is off (parked) for approx 1 hour, it will smoke after you start the engine? That is sometimes indicative of leaking valve seals. The oil pools around the seals when the engine is off, leaks down the valve, and burns the oil when you start the engine. You should definitely have a qualified shop diagnose the issue. Burning too much oil can prematurely damage the catalytic converters.
Your owner's manual might have something about changing the battery. They key for my Civic has a small screw that is really tight and was hard to get loose. Your key may be similar. Be careful if your remote has the screw because you don't want to damage the screw using the wrong size screwdriver
If the coolant expansion tank is overfilled, it will overflow when the coolant is warmed up. Make sure your levels are good (check when the coolant is cold). Even though the Check engine light went off, a DTC (diagnostic trouble code) is stored in memory. You should have a shop or parts house scan for codes. If codes are stored in memory, the car may not pass the next emissions/smog test.
A worn out ignition key can cause this problem too. Jiggle the key around in the cylinder and try to turn the key. If you have a spare key, try that because it might be less worn. Dealers can cut fresh keys if you have the VIN and can verify registration/ownership
If you know where cylinder 6 is located, try swapping that coil to another cylinder (just the part, don't rearrange the harness) and see if your misfire moves to the new cylinder. You'll know that coil is suspect. Also, if you just did your spark plugs, make sure the connector to the coil is securely connected. Did you replace the spark plug boots when you replaced the spark plugs? The boot from the coil to the plug should be replaced when the spark plugs are done. They get old, dry, and can crack when removed with the plugs. Consider changing the boots before changing any coils.
Maybe someone else can chime in but on some Toyota's, if you have the distributor a single tooth off, it can cause similar problems. I would try to get the timing sorted out first and then see if the drivability is still poor