Adhesives like Liquid Nails and Gorilla Glue are very good and have flexible applications. I would recommend taping off any areas that you do not want the glue to contact with.
I'm still confused on the the "flush fit"...do you mean that the window will sit inside the perimeter of the hole that you cut in the side panel?
Good luck, I look forward to seeing your results.
Here's the side panels Lian Li sells that have a window in them. They are quite expensive, that's why I'm doing the mod myself. See how the window is mounted inside and the edge doesn't have any covering or anything? That's the look I'm going for, but I want it to be square and I want to keep that side fan/mesh cover.