Running 35's you just wouldn't want to get on the skinny pedal much if you were on ledges or in mud, it might not be a good day. You can carry some stock shafts, but I find that a lot of people don't do that, it's just talk. It's pretty much a rule that 35's merit chromoly shafts front and rear.
Brakes are also an issue. It's a lot of rolling mass to stop, and stopping distance is important. It gets longer the bigger the tire, which I'm sure you know. It solves that, plus, it's very helpful offroad.
Do it in the order you want, but just know what is going on and why and make your decision. In the end you'll do it all it sounds like