Two thoughts on this - though I've never tried it.
One, if you need longer screws, and can't find them at your local Ace hardware store (mine is remarkable - the only screws I ever can't find are of really odd lengths, or odd materials, such as aluminum nuts so I can use them for router jigs), you can find just about any screw you can imagine at McMaster-Carr. They also have the single best search engine I've ever seen on a web site. Go, type "screws" into their search engine, and be amazed. It's really cool.
Second, I use a lot of Plexiglass (which is a brand name for acrylic, by the way) for jigs/templates/etc. in my day job. The best way to cut it is to get it close (I usually use a band saw, which is messy and awful; but score and snap works pretty well too, though it is slow), and then cut it to final size with a flush trim router bit. The big problem with using a Dremel and cut off bit for this is that so much of the bit is in contact with the material that you will always create a lot of heat (then again, I hate Dremel tools. The only thing they are good for is filling your dumpster!). The flush trim router bit will give you a better cut, and less of the bit is in contact with the plastic at any one time so you don't create so much heat, which means little or no melting. Just make sure you have already trimmed the Plexi kind of close to the box - less than the radius of the bit. Because of the angle on the edge of the box, it is probably a good idea to put a couple layers of masking tape on the sides of the enclosure so you don't eat away any of the aluminum from the box lid. That said, don't worry too much if you DO bite into the aluminum a bit - any decent router or laminate trimmer will do fine with a light cut on aluminum - just don't go too deep. Oh, and as always, make sure you push against the rotation of the router.
Also, it's really easy to polish cut plexi - use a blow torch and melt it a bit! It works great (seriously - that's the right way to do it. I'm not making that up or anything. Nothing else works as well! Just be careful), but you don't want to polish the edges for this purpose because the light needs the "rough" edge to be visible. Think of it as being kind of like a rear projection movie screen. Same basic idea. If the screen were clear, the image would just shine right through it, and you would call it a window.
Oh, and I'm sorry for being such a wordy bastard. I'm afraid its genetic.