Mask off every line you cut in your case and in the Acrylic if you use a dremel tool. With the metal nibbler there is no need to mask when cutting the window out. And to cut the Arcylic always leave the proective paper on until your ready to install it, here are some good directions: http://fins.actwin.com/diy/acrylic.html
It don't matter how handy you are the prefab ones always look neater.
Yes there are some crazy mods out there that look great but its the same with cars. you spend all that time making it into something it aint when you could have saved up and brought the one you want it to look like in the 1st place.