Spray paint is not only ok, it's probably the best option if you don't have access to a professional spray gun and an enclosure. Spray paint is what I use for all case modifications unless I'm spraying plastic parts and then I use a vinyl dye that comes in a spray can. Paint doesn't usually stick really well to plastic parts unless you prep them VERY well first and apply a good quality primer.
For metal parts, you should prep the entire surface using a clean, new, scotch brite pad and/or 400-600 grit sandpaper. Clean everything off well afterwards with mineral spirits or isopropyl alcohol before applying a good quality primer OR a self etching primer. Self etching primer can be obtained in spray cans as well at most home centers and hardware stores.
As for the acrylic side panel, that's probably not a good idea. A better idea would be to simply ENLARGE the window in the side panel using your acrylic sheet cut to about 1" smaller than the sides of the side panel and then gluing the acrylic in place using an epoxy adhesive.
There are plenty of tutorials on all of this online.
A few examples:
https://www.youtube.com/watch?v=jQqUAaKGRxI
https://www.youtube.com/watch?v=Q_YY83dGbEI
There are lots more out there too.