I can tell u that I have a 2010 with a 4" RE Supeflex lift on BFG KM2 35s (manufs actually run diff sizes on same 35 btw!). With soft top on I have 1 and 1/2" clearance at my garage door. Wanted 37s, but it wouldn't fit inside! With my hard top on it is more like 2". U should have no issues. Keep in mind a 35" tire may actually be larger, or smaller than that. BFG KM 2s run a bit small (34.2").
2010 JK. Rubicon Express 3.5" superflex, 35" BFG KM2s on Mickey Thompson Sidebiters, Poison Spyder Rocker Knockers, Poison Spyder rear Rockbrawler II bumper, Poison Spyder front Rockbrawler bumper with Warn M8000-S, AEV Snorkel, Spartan front locker. Oh, and tons of "Trail Tattoos!"