Water is the cheap and cheerful commodity that you don't really need any accuracy in measuring. You have either got enough or you haven't. Usually the former!
So set up your vertical clear pipe gauge away from the tank on any nominally vertical surface. Fill the tank and mark the level in the gauge; then pump out till it runs dry and mark the level again. Now divide the interval into four and you have a calibration for "empty, quarter, half and full". The gauge doesn't even need to be perfectly vertical.
Obviously the further away from the tank the gauge is the more that boat heel can affect it so you should install your pipe as close to the tank as convenient and make your measurements with the boat upright and steady and if the pipe extends far enough above the tank top it has no need of a bung to seal it up. After all the tank already has to have somewhere that the air can get in to replace the water which is pumped out.
That's the problem, the tank is under the v berth and there are bulkheads in the way so you can't see it. I like the clear tube as a gauge idea. If I can put it into a place easy to see it might be a good solution.