There are tons of built 4 doors and they go on difficult trails such as King of Hammers and Moab. If you feel like you need the room, get the 4 door and have no worries about it.
As for lifts, depends on your uses. 4" comes into expensive territory, needing to replace control arms for adjustable ones, replacing driveshafts etc...2.5" is plenty high to fit 35's. If you want to run 35's consider getting 4.10 gears or at worst 3.73 gearing. Shop aftermarket, don't get stuff from Jeep or Mopar, they are overpriced, rebranded aftermarket stuff. A lift manufacturer I suggest is Rock Krawler, don't let the name scare you, they are not "rock crawling" lifts, they are some of the best on road and off road preforming suspensions out there. A 2.5" Stock Mod (entry level) or 2.5" Max Travel (butter) would suit a mild build with some great off road ability.
Also call up one of the vendors on board. Jason at Krawl Offroad or Chris at Jeep Addons. Also River City Offroad is great too. I have all their phone numbers, PM me if you like for them. They can usually cut a good deal.
Rock Krawler Suspension, Inc.