Got stuck in deep, muddy water a while back, and the JK sat there for about an hour until we got it recovered (difficult location for winching). Got all the fluids changed as a precaution at first opportunity a couple of weeks later (diffs, g/box, t/fre case; they found a little water in the rear diff but all else was good). A week after the swim, I noticed the following:

When starting from cold, the gearshift feels completely normal. But once operating temp is reached, the shifter becomes progressively stiffer and difficult to move, it feels like the linkages are rubbing or sticking on something. At first I was concerned it was the gearbox itself, but recently when I was offroad I hit a puddle at speed and gave the underside of the Jeep a good spray with water; the linkage instantly felt loose and normal again and returned to the difficult shifting only after about 10 minutes when I assume it dried out, so I'm guessing it's a lubrication issue with the shifter mechanism itself. Other vehicles I've worked on in the past have a layer of grease on all the moving shifter parts which can result in a notchy & difficult shift if it wears off, so I'm wondering if this is the case here and the factory grease was thin & has washed off or there's mud/dust coating the contact surfaces, linkages, etc?

From reading this forum I know the internal shifter dust-boot can get stiff and cause restriction and difficulty in shifting, but apparantly this is when the box is cold, not hot. Haven't had the dust boot off yet, but is there lubrication access to the shifter when I remove it? It's still under warranty, but I'd rather know what I'm talking about when I talk to the service department at the dealer just so I don't get the old "can not duplicate" verdict. They didn't feel the stiffness when they had it for the fluid service last time, but I'm guessing it wasn't running long enough to heat up.

 

Have you crawled underneath the vehicle to take a good look at it?

You said a good spray seemed to loosen it right up, have you pressure washed the underside at a car wash?

 

bump.

What was the outcome. I may have the same problem.

 

So I'm reading that it may be the inner shift boot. I took off the outer boot and then the one under it. There is one more connected to the trans. How do you take off that last boot so you can get into the trans? My guess is water/mud/sand went in there.
So how do I take it off?