Wow!
First, this sounds like my problems way back. I could never seem to get rid of the water. The fuel gauge will never have anything to do with how the jeep runs - so that's a separate issue.
Draining the tank and blowing the lines is good. However, I didn't read what was done to the carb. It wouldn't take much to run good fuel through the carb to flush the water though. That would also apply to the blown lines/drained tank. Once done and good fuel added, that whole system would now be void of water.
Are you using ethanol gas? Do you purchase from a brand name or a generic quick mart? What kind of filter are you using and where is it in line? What kind of fuel pump did they swap in for your mechanical? Where do you park your jeep? Does it have a top?
FWIW, I've demonstrated that with enough STP gas treatment and HEET added to crappy gas, the jeep will run. But that also doesn't fix the problem. I'm next door in AL and its humid. It's rained what seems to be way more than normal recently and if your tank isn't sealed properly it could collect water. If there's no top on the jeep, any hole or seal (sending unit) could allow water in. If you park outside, people think it's funny to pour just about anything into a tank. Ethanol draws more moisture than non-ethanol. A low tank draws more moisture than a full tank.
What works better is: Ensuring all the lines are in good condition and properly attached, with no leaks. The tank, pump (and filter if added) and carb are all sealed from the outside and are checked for correct operation. Parking out of the elements if available.
Finally, if you had contaminates in your fuel other than water, i.e. gunk, rust, crud, etc. There may be some blockage in your carb. Could that be partly why your mechanics wanted to swap out pumps? When you drained the tank, what came out?
Concerning the dealer, I took my '95 XJ to the local dealer for service and they told me nothing over 20 years. Okay. Fine. No more sales from that dealer. I'd suggest calling first.
There are still some smart mechanics around that can work on these old systems - but just not as many. They may be hiding right close by. Have you tried a google search for, "Vintage Auto Service?"