1. If you're going to tow get the higher gears. You'll be glad you did and with an 8 speed transmission the gas mileage difference will be virtually nothing. On my Titan (I had two, one with tow gears, one without) and a 5 speed transmission the fuel difference was 1 MPG.
2. Yes, I would get a limited slip for $500. It turns your 2 wheel peg-leg truck into a 3-wheel bad weather/off-road monster. I have a LSD on my old Miata, and I used to drive it in the snow if it wasn't too deep because it was a better performer than a traditional two-legged 4WD that I always had.
3. I'm not sure what options are on the Limited but I like the Level 2 trim group, I remember from when I was shopping. It had more useful stuff than the Level 1 for me. But this is from memory more than a year ago.
4. I don't have E-torque. Guys that have them here either love them or hate them. If you are a techie it's probably right up your alley. For me, I'd rather not have that layer of complexity. If I lived in the city I would probably feel different.
5. Best way to get what you really want is to order it. You pay a little bit of premium, usually, if you're getting stuff the dealer feels like will be hard to resell, but then you get the truck you want, not what the dealer thought you wanted. I did not order mine, but I got the options I wanted and really don't care about the rest of the stuff.
Bonus question: don't order the tow package if you want the power fold mirrors. You can't have both.