Ran into the same problem on my wife's JK. First wheeling trip after the new goodies installed, shifting into 1st or 3rd, turned off the rear ARB locker. Not good. Our shop took the shifter off and bent it a little, then we ordered that billet trim ring from one of the catalogs, took it to an upholster shop and they made a leather boot. No more problems. I'll go take a pic and add it.

 

It's very easy to take the upper panel off. I don't remember for sure, but I'm pretty sure there are no bolts holding it in place. I think it's just held up by the side panels. If you pull the side panel on the drivers side, you can slide the top panel out of the passenger side. Just pull off the drivers side visor, pull out the one bolt on the side of the windshield frame and you should be good. Hope this helps.