Here is a quote from "thejuice" in another thread;

"i went with the limited because i noticed a lot less hood vibration. i was set on a trail, but when i test drove it the hood was shaking like crazy. i went back and drove another limited and there wasn't any noticeable vibration. my guess is the more aggressive tires on the trail transfer vibration to the hood."

Harper solved his hood flex/vibration with 3m film. He also suggests dynamat or the like as a possible solution.

I have an SR5, I bought the hoodliner for a Limited and installed it. Most if not all the hood flex, gone! I also have a bug shield which I think helped reduce the flex a little when it was first installed. (Possibly because it reduced air flow under the hood and maybe more support?)

Seems like a common cause/solution here? Add more weight/support to the hood, flex goes away. Be it 3m vinyl film, sound deadener, or dare I say, the factory hood liner.......just sayin. Be Safe.