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Have you actually crawled under the truck to see if your boot is torn? If you read any of the existing threads at all anyone who did the boot repair said it was a huge difference.Thanks for the input. I can still hear the noise after the truck warms up, so it might be something else. It might be a little noisier when its cold, but I mean cold engines are going to be a little noisy I guess.
The last post in this thread shows you where to look and what a torn boot looks like.

Check Yours! Engine Noise from Torn Steering Shaft Boot
Hi all, I just had had to share this old post from the 1st Gen Tundra side...its just too good to not. Anyway, I've been dealing with this exhaust noise coming from my driver side interior cabin when under any acceleration. It's been an annoyance that I've just lived with...and I'm willing to...
Long thread but some very helpful info. And the last page has some really good pics.

Engine noise filtering through torn steering shaft boot?
You better read this if you have lifted your Tundra with Tuff or RCD. For the past two years I have had a sound that appeared to be on the drivers side right beneath the floor board that sounded exactly like an exhaust leak. So naturally, I assumed in July of '04 that it was the O2/ exhaust...