First, I would recommend no more lift than needed for the tire/wheel combo - keeps the additional costs from suspension and drive shaft costs down and also keeps the center of gravity low...so, a 2.5 inch lift is all that is needed to comfortable fit 35s on a JK. Keep in mind the JK arms are already longer than the stock TJs were...so no need for a LA lift unless you go real big...no problems with DS at 2.5 inches of lift. As you said, if you want to go bigger than 35s, then plan ahead. Keep in mind that a "complete" lift with all the additional parts runs about $1,000 per inch. At 3.5 you are looking at adj control arms to set front caster and rear pinion, adj track bar or brackets, new drive shafts, esp in the rear not so much up front with the HP diff, extended brake lines, appropriate sway bar connects, etc. At a lift over 3.5 things can get messy as then you really need to start looking at relocation of spring perches to prevent spring bow, etc...
The 4.10 might work for you unless you are into rock crawling, etc, then you would want to look at a regear IMO at 35 or 37 in.
And, when you get at a 40 in tire/wheel you will definitely need regear, upgraded axle shafts, beefed up axle and diff housing, etc, and probably a hydro assist steer kit...just my O though, and, more money!
08 JK 23S - Colorado Jeep Club No. 204
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