[Digger84]

Sounds like his clutch is not releasing

If it won't roll freely in a low gear with clutch all the way down the. That would be my guess

Find a flat parking lot away from everyone shut the jeep off and with transfer case in 2 hi and tranny in first and Park brake off and no foot on brake pedal now with clutch pedal all the way down still no brake and leave tranny in gear and crank the starter.
Does the jeep move forward when starter spins the engine?

 

[Digger84]

With slight drag of clutch brakes will win so if park brake set or foot on brake even with drag it won't lurch forward so what does it do if you try what I posted

 

[Digger84]

With clutch in (pedal down) it should roll freely and tranny gear should make no difference

What a higher tranny gear does is require less engine spinning for a given roll speed with clutch pedal up

Think of if as a lever arm
In low gears like 1st or reverse engine has big lever arm over wheels and wheels have small lever arm over engine so easy for engine to spin wheels and hard for wheels to spin engine

In high gear like 4th or 5th exactly the opposite

 

[Digger84]

I figure the gear difference in free roll means clutch is not disconnecting tranny from engine completely and that slight drag while not enough to lurch jeep forward with starter is enough to screw up shifting

So I am still betting clutch drag issue possibly related to damage from operation under water maybe clutch plate is swelled thicker

Good news is tranny is probably ok but bad news is that either way he is gonna have to remove tranny and replace damaged clutch components

But never a good idea to drive a vehicle you like and plan to keep thru deep water unless a true emergency with no choice