Sounds like you will need to get rid of that extra liner, but FIRST, decide if you might possibly want your waterfall to extend a little bit farther back. If that's a possibility, then keep the liner for now, fold and tuck it. If you have no room to expand, then probably will need to cut it off. Just make sure you have a good seal of the liner up against your tank, pull it up to below the weir, and you can tack it to the tank or seal it to the tank, just in case any water falls over the edge of the weir. There are times that may happen, for instance if something clogs the weir and the water spills over the edge. Shouldn't ever happen, but I had it almost happen because I put floating plants in the filter tank, and the water was not flowing freely out of the weir.
And, good luck to your hubby with the shelf cleaning.
It's always worth the trouble to try. Good thing is if he finds it more trouble than he wants to deal with, he can always remove them.