I dont understand the apprehension about drilling through the acrylic? I just finish a sump and drilled hundreds of holes through acrylic. Granted it was only 1/4" thick but thicker acrylic would be a little harder to drill through but less likely to crack during the process. As far as the other question, I would increase the notch for the window to sit in so there is room for the liner. The pressure from the acrylic to the liner will give you the seal, it creates a gasket. Thats why the screws are needed to draw the acrylic into the liner.