Oh you bought extruded acrylic instead of cell cast. You got the cheap crap. Those baffles are probably going to warp. That tool you bought is not a good tool for making cuts with. With the thin acrylic you bought you may get away with it. They are just baffles so if they warp or pop out it’s not going to cause a flood if it was a tank I would say take the acrylic back. Where there is acrylic on acrylic I would use weld on to get a better bond. How much did the acrylic cost? I had a glass shop cut and sand my baffles to size and it only cost me $30. With everything my sump cost $60 to make that’s the tank baffles with them cut to size and the silicone.
Also, I plan on using weld where I can. I've done some acrylic work in the past, but mostly repairs and the such. Nothing this extensive.