The biggest danger when water goes in the intake is hydrolocking, if that happens your toast. You said you drove it three miles afterwards so chances are after a complete fluid change you will be ok.
Do you have your diff vent lines extended up into the tub?
if you go onto www.jeepkings.ca they have plans for making your own snorkel.
I once buried my old 1980 toyota pickup so deep water was splashing over the hood. the only long tern damage was the passenger door rusted bad. My brother tried to open the door instead of climbing out the window to through a strap to my buddy