As OffRoad Treks suggested take it out how it is built now and play with it. One thing to NOTE: You want to lock your rear lock the minute you get off-road since the limited slip portion of it is known to be weak and can break. So you want to lock your rear locker at all times when off-road. If you do a search on here you'll find it discussed.
To add to what Trek said, don't build past your skill level. Learn to wheel it as is then when you find yourself pushing past what your rig is capable of then modify more.
And like Tworley said determine what tire size you're going with and then pick your gear ratio.
As to if running 35" tires on a SWB rig is not safe? There are many here who have done so without any issues. I was at one point running 38" tires on a 95" WB TJ. They were short 38" tires though.
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I'm now sitting @ 100" WB and 38x13.5x17 tires.
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