Good pics/write up. My install was very smiliar. I like the lexon cut piece. I want to do that to mine. It'* har to tell from the pics, did you go down the side piece too. I'm also thinking about insulating the box with that silver stuff. I won't do the top clear piece of the box though.
I totaly agree with you about the cost to the thrasher box vs. creative mechanical abiltity. Not to sure it was worth it the cash but sure looks nice though.
As to the MAF screen issue, I removed mine and the only intake mod is gutting and opening up the front end of the stock airbox. Everything runs fine and has for a few months (since my join date , whenever that was). I felt an increase in acceleration and general power pretty much right away. No numbers to prove anything, though.
I still have the screen safely tucked away, though, just in case.
Don't know if this helps as I have a 98, but I figured I'd chime in.