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Transmission and CEL issues with a 2006 Jeep Wrangler Unlimited Rubicon

Problem #1… 2006 Jeep Wrangler Unlimited Rubicon…I purchased it December 2011 with about 50,000 miles. It has a flood title as it appears to have suffered some water damage a couple months prior to me aquiring it. The Jeep came from the Massachusetts area and it is living in Iowa now. I believe the water was all the way up to the rear view mirror because it has water damage spots in it. A few weeks after I purchased it I began to notice a grinding when I shifted from 1st to 2nd and from 3rd to 4th. I took it back to the dealer and they ended up replacing the clutch and flushing the transmission fluid. That seemed to fix it for a few months but then it came back. Also, if I keep the clutch pressed in for about 1 second or 2 and then shift it into gear it doesn’t seem to grind, but with a newly replaced clutch and just over 50,000 miles I don’t feel like I should have to do that. Currently I have about 53,500 miles on it. I don’t drive it that much because I have a company vehicle. I bought it “as is” so I cannot take it back to the dealer. I’ve heard that maybe the synchronizers might need to be replaced which would basically constitute a transmission rebuild. I’m trying to avoid that. It has the 4.0L straight 6 with the 6-speed NSG370 manual transmission.

Problem #2…I also have the check engine light on and the code says its an issue with a “leak” somewhere in either the exhaust system or it could be the gas cap. The gas cap is aftermarket locking gas cap, not OEM. I have read some other posts dealing with this CEL issue and will try the oil around the seal or just replacing the cap with an OEM cap from the dealership. When I fill up at the pump and lock the nozzle it always overflows and gas spills out onto the paint and onto the ground. Whatever the mechanism is that shuts off the pump before the fuel overflows does not seem to be working. I also suspect that this issue was caused by the flooding, screwing up some sort of sensor.

Other than these two issues I love my Jeep and will probably always own one. I hope somebody out there can help. Thanks.

A few weeks after I purchased it I began to notice a grinding when I shifted from 1st to 2nd and from 3rd to 4th. I took it back to the dealer and they ended up replacing the clutch and flushing the transmission fluid. That seemed to fix it for a few months but then it came back.

I’d suspect the fluid exchange did more to temporarily eliminate the synchro issue than the clutch work. You could do another fluid exchange and eliminate the cast off material from the synchros again but it’s usually diminishing returns for each time you do that.

Also, if I keep the clutch pressed in for about 1 second or 2 and then shift it into gear it doesn’t seem to grind, but with a newly replaced clutch and just over 50,000 miles I don’t feel like I should have to do that.

It’s not likely to be the clutch but considering the effort and money involved to rebuild the trans, it would be worth checking to be sure the clutch is properly adjusted and working.

I’ve heard that maybe the synchronizers might need to be replaced which would basically constitute a transmission rebuild. I’m trying to avoid that

Good luck in that quest. Bear in mind, there are some fairly hairy 4 wheeling areas in western MA. Not to mention all the trails in NH and ME which are a short drive away. People usually lust after the Rubicons for what they can do off road. They usually lead a fairly rough life and need lots of TLC to bring them back…

Why did you purchase flood title car?
What is the code that you got? It sounds as if your evaporative emissions system is not functioning properly. You might have a bad vent valve. Do you go offroad? Is there a lot of mud/dirt underneath the car, near the filler neck and fuel tank area?

The fuel filler neck assembly could be responsible for problem #2

The price was good for a Rubicon Unlimited even though it has a bad title. I had it checked out very thoroughly by two different mechanics. It was very clean and had/has no leaks. There is only so much mechanics can see giving it a once over but other that these two issues I haven’t had any problems so I feel confident they gave me good advice. I do not go off road too much as there really are no trails near where I live. I do play in the snow when I can though. So how can I check if its a bad vent valve? Do I need to drop the tank? Can the fuel filler assembly be replaced without dropping the tank? I will get the code and post it soon. Thanks for all your help.

Evap components should be accessible without dropping the fuel tank, but I’m not familiar with your exact car.
The fuel filler assembly should be removable without removing the tank. But you’ll need to be able to get your hands on the top of the tank to undo hose clamps.
This is just general advice I’m giving here, as I’m no Jeep expert.
I have seen fuel filler assemblies AND vent valves cause problems filling the tank, by the way.
You may want to seriously consider paying a certified mechanic to get involved. Evap problems (if that’s what you have) are sometimes challenging even for the full-time pros. And they have the knowledge, equipment and training.
I’ve seen a lot of guys throw parts at cars without fixing the problem, only to pay someone else to diagnose and fix it later.
All in all . . . just more food for thought.

Ok so I hooked up a code reader and I got the following:

P0153 02 Sensor circuit, slow response bank 2 sensor 1
P0457 Evaporative emission control system leak
P0456 Evaporative emission control system leak

Can anyone tell me what this means in English??
I already ordered a new gas cap. Maybe that will help with one of them.

It sounds as if that oxygen sensor might be sluggish.
So you do have a problem with the evap system, as I thought.
These codes indicate that the PCM (your powertrain control module) sees that the evap system isn’t sealing.
That new fuel filler cap might help with p0456 and p0457, but the cap doesn’t come into play when you’re filling up . . .
I still recommend going to a Jeep mechanic to get that evap system diagnosed and repaired.

Well I guess I will change the oxygen sensor and see if the new cap helps before I take it in the shop. Thanks.

Thanks for the continued updates.
Please let us know when it’s finally resolved.