Am I safe to cross water up to the airbox?
Extend your rear diff breather and keep your speed. Don't sit in the water. As for the alternator, I've been over the bumper in dirty water with 2.5 lift and 33s, stopped and backed out, still works great. Just be aware that the fan will throw dirty water all over the compartment when it comes on, the belt will be soaked in dubious water, and your exhaust manifolds may be in the water as well. Personally I wouldn't go diving over about 3/4 tire height...I guess that's about two feet, two and a half feet...also there is a very large resistor in your driver's side wheel well. It gets extremely hot, and it sits outside the engine compartment. Don't get it wet. I forget exactly what it is, but IIRC from what the tech told me it's part of your fuel system electronics, and it is possible to crack it with very cold water if it's very hot, then your engine dies. Maybe somebody can chime in...it's not a big deal for you, since you have a wheel well liner, personally I moved mine. Just don't sit in water over your front bumper.
What is the maximum height of water that a stock truck can cross with relatively no worries (other than being pushed downstream or getting water in the cabin)?
Until something shorts out, or you suck water, whichever comes first. Look in my main gallery for shots of the passenger side, look for a big round hole at the front of the inner fender. That's where your stock air tube takes air from the wheel well. Any higher and you're sucking water.
On a similar note, has anyone rhino-lined their interior?
I used Herculiner. It's less of a pain in the a5s than spray-in liner, because you don't need to mask everything...but prep is similar, and you can do Herculiner in the garage, vs having to strip and mask the interior and then somehow get it to the spray-in shop, if they'll even do it. Most wont. I did three coats. Overall I like it...put Husky liners back in, front and rear, put the base/storage under the rear bench back in, all the plastic went back in fine, but I'm not done...going to ditch the vents at the back for something lower profile, and need to seal a small hole I made while removing the OEM jack tiedown from the driver's side rear box. Couple other small things as well that need to be addressed, all minor.
It's louder with the vents open...they're stuffed them with closed cell foam now, it's much better. It's warmer too, no insulation over the driveline tunnel anymore and a belly skid means more heat in the cabin. Maybe not so good in 100* heat, but I plan to do the Sequoia auxiliary A/C fan mod this summer.
I've just uploaded three pics of the mostly finished product to my main gallery.
-Sean