The jumping TOD, lights and all, would be normal on sand if you are NOT in 4WD. That is the TOD doing it's thing. As the TOD computer detects wheel slip (spinning in the sand), it will throw power to the front wheels for a second until it doesn't detect wheel slip, then it will pull the power back. If the wheels slip again, it will throw power to the front wheels again, hence the "jumping" sights and sounds. The TOD doesn't usually keep power at the front wheels unless you are doing some serious slipping around.
The grinding noise may be the fact that you are low on transfer case fluid. Mine got a little low in Moab last year, and it seems that you can hear the gears meshing. I would check the transfer case fluid pronto.
If the clunking isn't harsh when you put the VX into gear, it's probably normal. With over 100k on it the drive train parts probably have a little play in them so when it goes into gear things may move a little. If the VX slams into gear then you may have a mode selection switch problem.
The clunk you hear/feel as you come to a stop may be the slop in the drive train again. I know as I decelerate at a stop, the transmission shifts down into first and the VX, sometimes, noticably lurches as first gear grabs. Kind of like engine braking in a standard.
Hope that helps.
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