You will be fine, you will just be using 4low much more often offroad. I've ran 3.73s in my tj and lj on 35s for a while until I went to 4.88s. I have yet to break anything but u joints on d30 and 35s, no need to upgrade for light wheeling unless you lock it. Steering would be a high priority for me, the stock set up is horrible.
Control arms depends on lift hieght not so much tire size (though I have bent stock upper control arms).
I haven't had any issues with stock linkages after completely pulling them off, straightening them, and adjusting them properly... But I have heard of issues. This one may work with modification? http://www.boostwerksengineering.com/231-HD-Shift-Linkage-Auto-Trans-_p_25.html