NEVER, for the love of God, never use those kits. The molding is massive and ugly. That's my opinion. Look back over my Case Log and see the first window I had.
I just went to my brick and mortar (TrueValue, Lowes, HD) store and bought a 30x30 sheet of plexi (1/8th thick - You can also use 1/4 for a stronger window). Also, I bought something called "Allen Key Bolts"
. 10 of them, and matched 10 nuts to go with those.
Then from FrozenCPU, I bought some C-Channel molding
(I bought 6 feet for also cleaning up the modded edges on my case). That molding works great for stopping vibrations and looks excellent with my current window.
^^^ EDIT: I'm sure you can pick up essentially the same molding from your local B&M store. Just make sure it's rubber and not plastic.
From there, it was all work. You can see progress pictures, also in my Case Log. I taped up the metal to prevent scratches, measured things up, and began cutting the metal. From there, I cut the plexi to fit inside the metal guides that help the panel go on. I VERY CAREFULLY drilled holes in the plexi and the metal for mounting. Tack-clothed both items, mounted it, tightened the bolts, and dremel'd the ends of the bolts off to keep from having mounting interference.
Case Log - CM690