Well I'm in the process of doing a window mod now...and I too can get plexi free...lol...legally of course

! Anyway for the window you are gonna need a few things...ruler, pencil, drill w/ a bit capeable of drilling steel (most of them won't have a problem), Jigsaw with a fine metal blade...I believe you should look for about 22teeth per inch...or look for one that says for thin metal (they will help you at the hardware store). Draw the size you want on that sucker with the pencil and the ruler...drill a hole somewhere (near the outline) inside where the window will be. Then insert the blade of the saw into the drilled hole and get sawing. If you're painting it scratching the finish isn't a big deal...but if you want it's best to cut on the inside of the case so scratches from the base of the saw are on the inside. You can also put some masking tape on the foot of the saw.
Other than that molding at auto zone ran me $3 for black stuff w/ glue already applied. Double sided tape ran me about $3 also for plenty to do the window on a single case. You may have all the tools around the house which would make it a lot easier. Also, you can do this with a dremmel...but a jig saw will look much better and take a hell of a lot less time. Believe me those metal blades cut through computer case steel a whole heck of a lot faster than "reinforced cut of discs" made of fiberglass. Oh...and if you already have the jig...metal bladed are less expenisve than those dam disks...and you won't go through 10 of them cutting one window.
As far as painting I have been airbrushing on and off for a little while...but depending on what you want to do I know rustolium (sp?) works rather well. You can get nice results out of a spray can if you take your time and mask areas and the like. You can do nice fades, etc... with them also. I think rustolium is like $5ish a can. You could probably get away without sanding and priming since the metal is already painted once. For a nice gloss finish use a clear gloss that matches the type of paint you used (ie if you use rustolium...use their clear gloss). Apply it spairingly but in a few coats. Try to get everything nice and even. Also a tip when spraying anything...well vented area...blah blah blah...make sure you put stuff down b/c the spray will get places you never would think....and start the spray a few inches off the project and then make a clean stroke over it. Don't start spraying right onto the project you will get blotches. Painting should run you less than $20
I would go with a cold cathode ray tube for lighting...they are nice and bright and not too expenisve.