Just a quick re-cap on our setup so I can get some more specific opinions:
31" TSL's (will be 35's at some point)
High steer and spring overs
YJ spring swap with RRO HD shocks, missing links up front (front leaf mounted) and soon to be on the rear.
MS1 running a rebuilt 1.6 16v

We went riding last night and ended up getting into a mud hole.  Basically I have water in the gas tank from what i have established so far.  My front end was not swamped... my rear just fell into some ruts to where the entire tank was under.  And as Murphy would have it... I had a full tank of gas.

Anyway, I want to be absolutely 100% sure this will never happen again.  I know there are vent lines for the tank that can be raised right off the bat.  What Im not sure of is whether the tank filler hose clamps and other clamped fittings are very reliable.  Again, I want 100% total waterproof gas start to finish.  I was thinking of a fuel cell but I will definitely have it under-mounted due to needed the rear cargo/passenger space. Additionally, are there any other weak points I should be focusing on? 

TIA

I could be way off but my guess would be a bad or lose gasket on the fuel tank sending unit, other than that maybe a missing hose up there. My friends and I have run our Samurais thru very deep water many times and have never gotten water in the fuel tanks

You didn't post what year Sammy?
Anyway, check to see that all the lines are good on the Charcol Canister.
and the return lines to the tank.

CAPT

Propain conversion......The only guaranteed watter proof system I have ever seen....Boxcar...

All fuel tanks should be " water proof" or at least water tight. If water can get in , gas can get out. You've got a leak somwhere.

If you want to spend  bit here's the answer for you...

http://www.zukiworld.com/forum/classified-ads/petroworks-15-gallon-gas-tank-with-fuel-filter-and-internal-suzuki-fuel-pump/

Look. All gas or diesel tanks vent to the atmosphere, Otherwise as fuel was pulled to the engine a vacuum would be caused which would stop the flow of fuel...It stands to reason that if air can enter watter can enter.
 Most fuel systems were never designed for submersion in watter.
 I tend to agree with a previous poster that your seal at the sending unit is possibly the culprit. Or the gas cap itself..
Once you have sorted that out , I recommend raising the vent line  from the tank.

Not sure what exactly the culprit was but I replaced all the factory clamps with worm types, new hoses, and resealed the sending unit.  She is air (water!) tight now.