I personally would drive it stock for a while and get a feel for the rig. Get some AT tires for the kind of driving you mentioned.
It all depends what you are wanting to do with it. If you say 90% is day to day stuff - what is the other 10% going to be?
IF that 10% is gonna be forest roads, with some rocks (not Rubicon rocks) or a lot of trails in Moab, Death Valley, Anza Borrego, Engineer Pass, Schofield Pass, Black Bear Pass, Pearl Pass, Monache Meadows, Coyote Flats, Silver Canyon Road, I think 32's-33's will be sufficient and not worry about having to re-gear.
Minimum would be to have skid plates either from ARB or CBI Off-Road that Alex had done and I think its about 4 weeks out from my last call to them, or Asfir 4x4 from Israel with a $586 shipping and handling charge. A rear bumper if you don't mind having to open the tire carrier each time you want to access the rear. Slee will have a rear bumper soon too.
If you can get away without the third row seat - then maybe some ARB drawers to put tools and spare parts in safely. If you want some drawers that can be removed, then maybe some custom made ones that can be strapped down safely using the third row seat slots on the floor. Removing the third row seats are only 3 bolts per seat.
Suspension - there's a few options. Slee, Kurt, Paul can all advise you on spring rates with the load you want to carry. A few people on this group has done the same you are wanting to do.
OR.....
35's with some lighter wheels to offset the unsprung weight and rotational weight, different offset wheels too. ARB lockers with 4.88 gears, some BP51 shocks or ICON's. OME springs. Skid plates, front and rear bumpers, winch with synthetic lines, drawer system, fridge, 2nd gas tank, rear tire carrier, jerry can holder, dual batteries, LED lights, Big brake kit. You can also have 2 sets of wheels - one AT for everyday and some more aggressive mud terrain tires for certain trips. TRD supercharger - suggested rebuild every 100,000 miles. 500hp. WOOHOO.
If you want a rooftop tent to sleep in or a trailer like Romer. While we are at it, you can also add the long travel front IFS suspension that Brian did using Tundra front suspension pieces.
Please update us on what direction you go. It will be fun to read about it and hear about your experience.