I think re-sealing a tank and re-building a tank are two different things.
Re-sealing was mentioned above. Removing inner seal and keeping the silicone that is wedged between the panes of glass.
Re-building would be to remove all of the silicone including the wedged silicone between the panes of glass.
As mentioned in a similar thread. You'll want to use something like thin guitar string (metal kind) to pull it through the silicone. Be patient.
Also remember if you are going to use a tile saw to cut the glass.
1) Make sure you use a diamond encrusted or electroplated blade. A carbide blade won't do it
2) When moving a LONG piece of glass through the blade make sure that it goes through straight. It sounds like it doesn't really matter to you because it will be your top edge so it doesn't have to be straight to butt up against another piece.. but I think that if it binds while you push it through the saw it might break from the pressure.
I think that cutting it would probably be a better bet.
OR
just live with the 2" height.
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