My personal opinion in the matter is not to cut or alter the glass baffles in an operational sump/aquarium. Why risk the following.
a. injury/cutts/infection etc.
b. increase possibility of damaging the side panels of the sump (while its still holding water)
c. small shards of glass left in the sump afterwards.
I'd purchase a new tank/sump, make the conversions your intending to have and then replace it with the existing one. It's a little more effort and cost, but why take the chance.
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