OK, while trying to get my o2 sensors off I noticed something!! What appear to be breather tubes just dangling.. I pulled the hooked end up in to the engine compartment to see if there was any obvious connection, this is NOT the axle breather tube. Then went underneath and found the other end of one, which reaches the xfer case, isn't even plugged in. Does anyone know what these are for? They don't seem to match up to the EVAP system:

I pulled this one down, it in between the tranny and front driveshaft connection at the xfer case.


Right above the o2 sensor passenger side:

 

They are breather tubes. The hooked end is routed up the firewall and terminates just behind the engine. The other one comes up from roughly the same location and makes a 90 degree angle and runs horizontally along the firewall. One is transmission, and the other xsfer case, IIRC.

 

The o2 sensors wouldn't keep your engine from running, neither would the breather tubes being clogged.

On the senors, make sure you're using a 6pt socket and not a 12pt.

 

Socket? on O2 sensors? I used a 7/8 open end wrench. Did not think a socket would go on there.

 

I tried two different O2 sensor sockets on mine when I did them ~40k ago and couldn't get enough leverage without the sockets starting to slip over the hex on the sensors. This was after I had been soaking them for days with PB Blaster. I finally cut off the connector and slipped the box end of a combi wrench over it so I could double up on the wrenches for more leverage. Finally broke them free. Antiseized the crap out of the new ones. With the open end of a combi, you only have 2 flats against the sensor...

 

Mine came off with a little effort, was expecting it to be a bear, to change the two upstream out. It literally took 10 minutes to do both, the new ones are coated with anti-seize.x

 

The breather tube for the transfer case connects on the top of it. There is a banjo bolt up there, the tube connects to a collar, the bolt goes through the collar. Like someone already said, those tubes wouldn't be the cause of your engine problems but they are still important to keep connected and cleared out. In high water/mud sucking that into a diff, T-Case or Transmission could be costly.

 

They won't, except he was talking about cutting the wires off as a last resort.

 

Even with good breathers, sitting in deep water for very long can ruin the clutches in an automatic.
A guy in canada had that happen. He ended up replacing it with an R380.

 

You might want to take a close look at the fuse box under the hood. Maybe it got water in it and was slowly going out as you drove it after you got it unstuck. I really think that you have some sort of electrical issue going on since you are sure you have good spark and fuel pressure.