From what I can tell, working with plexi is a trick unto itself. The ability to make straight clean cuts, bore clean holes etc without chipping/cracking. Certain blades or bits need to be used, the area to be cut needs taped off to prevent shattering. A hand drill isn't really appropriate if looking to make fan holes. There are places that sell hole saws in the proper sizes for various fan sizes, but they're spendy at around $40/ea. Should be used in conjunction with something like a drill press to prevent wander/chatter etc. Dremels work but tend to leave a rough finished product. Even jobs I've seen a lot of skilled people do with a dremel, it's kind of like building fine furniture with a sawzall. Unless there are other cover pieces like a milled fan shroud to cover the edges, it looks like someone diy'd it to death.
For finishing the plexi edges you might have better luck with a small propane torch. A matter of being careful not to melt it to the point of making a straight edge 'wavy' but enough to get rid of the roughness from a saw cut. Sanding it doesn't really do that. Using some sort of router to 'ease' the edges and put a very slight chamfer on the plexi can help prevent chipping/cracking.
I agree with Mr5oh about using the existing side panel and cutting out a window. It will still likely end up looking modded if using rubber channel as a gasket between the cut window hole and the plexi but at least it will be a better finish. It's very difficult to get a 'finished' look like many case manufacturers achieve since they usually skip the rubber gasket and instead the plexi window has been routed (more likely molded since they have all the fancy toys for manufacture) creating a raised portion in the plexi window the exact size of the window hole. That way when the plexi window is installed, the surface of the plexi nests into the window cut out and becomes flush with the case door for a real finished look.