Howdy and a big WELCOME from Nevada!
Quite the list you have there. You don't mention what gear ratio you have in your differentials, but going with lockers and big tires as you mention, you may want to include the cost of a re-gear as well. For difficult wheeling like you will encounter on the Rubicon, I'm pretty sure you will want lower gears than come stock.
You don't mention any skid plates beyond rock rails... feeling lucky? IMO, lower control arm skids for the front are MANDATORY. They are very vulnerable on your JK. You should consider transfer case, evap canister, and perhaps an oil pan skid. You stock gas skid is tougher than most folks credit though it will get beat up.
As far as that warranty thing goes, good luck! You can read nightmare stories about warranty claims and modified vehicles, especially when the purchaser thought they would be covered by the warranty. Breakdown someplace away from your dealer and see what happens for starters... Even your dealer may start pointing fingers if things break even if he is the one that did the install. Just keep in mind it's not his parts, just his labor.
I'll not comment on your lists price tag. While you could probably save some big money by purchasing your modification parts from different sources and doing some of the work yourself on your new hobby, there is something to be said for the convenience factor of just having it done.