Congrats on getting a great deal on a great truck. Sounds like you are looking at more functional suggestions rather than performance suggestions, and that's probably good since you are still in warranty.
There have been good words said about
Katzkin Leather Interiors
Here is a site to buy, but you may want to shop around
TOYOTA TUNDRA ACCESS CAB Katzkin Leather Interior (2 row)
Several folks are buying the 5100 Bilstien Shocks to level their trucks. $90 a shock plus an alignment. So if you do the install yourself you looking at just under $300.
I use 3M Scotch Guard for stain prevention.
And Ozium deodorizer for any stinkiness.
You may want to look into a Scanguage II. You can get them form
amazon. Click the link in my sig to find out more on that one. It's nice if you don't already get instant readout on gas milage and other engine info.
Linex is a great idea.
A bed cover is good too. Lots of opinions on that one. I'm looking at the Bakflip HD. Leer and ARE make great units as well.
You'll need to replace OEM tires at about 35-40K miles, so be thinking about that. If you want to go bigger there is a lot of research already on this site. If you are staying stock best tire is probably Mich LTX. Good bargin tire is Yokohama.
On the bling factor, I would suggest getting an exhaust shop but dual tips out the back. You may or may not want to keep the factory muffler. Click on my pics and you can see my Fualy set up. Dual exhaust on our trucks kills your power but if you dual it south of the muffler (Faux Duals) you won't have a problem. Looks really nice, I think.
Hope that helps.