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:

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I had a Dremel tool on hand to cut through the air box, but had to purchase a bit for the material, again, Home Depot, Item #080596035242-194.

Just used the sand paper drum bit to clean up the edges, and to shave off the inside ribs of the air box surrounding the hole. Some sensor safe Permatex from Advance Auto to make a gasket seal, and I was good to go...

Here is a shot of the finished product mounted back in the truck:

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As stated before, I chose to order "plugs" for my stock intake, and was able to find what I wanted from McMaster-Carr.. Here are the additional parts that I used:

1: #9277K34 - Silicone tapered plug, 2 31/64" large end ID
1: #9277K31 - Silicone tapered plug, 1 49/64" large end ID
1: #9277K75 - 5pk of Silicone tapered plugs, 1 1/64" large end ID
1: #45945K32 - 316 Stainless smooth band worm gear clamp 2"-3", 1/2" width
1: #45945K31 - 316 Stainless smooth band worm gear clamp 1 1/2"-2 1/2", 1/2" width
1: #45945K66 - 316 Stainless smooth band worm gear clam 1 1/16"-1 1/2", 1/2" width

...and for the redirect of the 7/32" ID hose originally going to one of the removed intake boxes, I ordered a 1/4" tube ID Tee #5670K31 - type 303 Stainless barbed fitting. The 7/32" ID replacement hose I found at Advance Auto as well...

Here are pictures of the three plugs in relation to the intake:

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I used the worm gear clamps to keep them in place... All in all, I was happy with the way it turned out.

If anything, I would have liked to go a size or two bigger on each of the plugs just for a slightly snugger fit prior to using the worm gear clamps. However the clamps used had plenty of adjustment, and the silicone plug material formed nicely to the slightly out of round clamping force the worm gears provided.

From these next pictures you can see how little the plugs protruded into the intake hose, and what the final installed hose looks like:

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