My PRU lid is slightly proud of the center of the side glass top pieces. The lid seems dead flat on mine. Might be some other issue for focus and registration. Hope you get it resolved.
I’ve had very good success with placement of images over scrap pieces of material and using even very small pieces so anything that out of placement is a bit strange.
Do you have some type of test image that you can put over cardboard and give a good benchmark of what’s going on now?
This topic has lots of good discussion of camera alignment and a few good images of what to expect from a few months back.