My Daughters 98  4.0 LHD Wrangler (Auto 2" spring lift, 2" spacer lift and 1' body lift) is having transmission issues. My tranny knowledge is non existant but willing to try anything twice.
  
it seems during the last wheeling  venture,  my daughters  Jeep had kicked itself into 2wd while she  was in mud lake, three times had to be towed  from 3 foot of muddy water (shifter linkage hitting the floorpan since the last lift)  
A bad  intake connection sucked the lake into her  transmission. Didn't  find out till later in the day. We drained the tranny  flushed it and changed the filter . total of three times now. 
Ended up that it couldn't take off in drive, had to drop it down to 2 or throw it into neutral then back into drive in order for the  vehicle to go forward properly. 
Following day on the  way home from work, she  couldn't switch it in and out of gears like that, and it sounded like it was racing and barely moving forward at all. At the next stop, (10 feet from the first)   she was able to get it to shift  2nd to D to get it to work, but this time, it didn't. No matter what gear it was   it in, the Jeep was in wouldn't . move and had to be towed home. 
Any suggestions to how I can help get this back on the road. Her Boyfriend has purchased a rebuild kit for it, but I  am hoping we missing something before it gets torn down?
Does this sound like A NSS issue like the GC in the adjacent thread. Or is the water a step in the other direction?
Cheers. .     Martyn