Yeah, I did a cheap used 4.0 TB swap about 4 years ago and had all sorts of problems with it. Just pulled the thing and went back to the 2.5 for about 3 years. Then, ultimately, picked up a fabricator job on everbody's favorite over-charging auction site. This bored out 62mm job at $100 seemed to work ok this time -- not sure why though.
Just that, with any of the mods you do to a 2.5L on the intake side, you are not dealing with a Mass Air Flow sensor. Instead, the engine is going to adjust based on Intake Air Temp (IAT), Manifold Air Pressure (MAP) and RPM.
So, if you open up the intake with a 4.0 TB + some kind of cone filter on a three inch metal tube, your MAP levels are going to drop and you are going to run lean -- low end torque is affected. Furthermore, you may "lean out" because your engine is sucking more hot air, too (not that the original airbox set up was any kind of cold-air magnet, itself ).
The solution to this with the no-aftermarket-chip 2.5s is to use an adjustable MAP sensor from Turbo City or elsewhere. This will help you manually richen the fuel curve after you add intake upgrades. Other thing to do, of course, is use some kind of CAI kit, so at least hot-air won't be screwing you up to bad. Don't think the new JKs have this issue like the YJs and TJs do -- think JKs Caravan engines use Mass Air Flow.