I know there have been plenty of posts about these mods, and I thank everyone that contributed...especially those at:
Intake Silencer Removal Mod - 3rd Gen 4Runner (2000) - YotaTech Forums
I followed the steps listed in the above link and chose the "Option 2" that was suggested for the ISR mod...basically because I was able to order the parts online and do everything in less than three hours... Sure, my finished product does not look nearly as OEM, or clean as the "Option 1" that was shown in the link, but this worked for me...
The Deck Plate Mod:
I chose to order a 4in deck plate from JMS Marine supply, no reason, just was the first I found online. Shipping was a tad high, but I am happy with the product:
Beckson Marine Deckplate 4In Black Non-Skid BEC-DP42B BEC-DP42B.
Instead of using regular window screen to guard against debris entering the air box, I ordered a section of 316 stainless steel 15x15 woven mesh from McMaster-Carr - since I was going to be ordering other items from them anyways. The mesh came in a 12"x12" section that could easily fit two or more deckplates in case I made an error. This material was item #9319T148.
The stainless steel clamp I got from Home Depot - Item #0000-100-530, along with the stainless screws needed to attach it to the air box - Item #0000-104-971.
Here is a picture of the mockup prior to trimming the corners, or installing within the air box: