All I can think of that can cause the alternator not to charge, after you have replaced your alternator twice, is a bad ECM (engine computer). The alternator's voltage regulator is contained inside the ECM module. If you want to replace it, you can usually find rebuilt ECMs for sale on eBay fairly inexpensively.
Personally, I would not install a 4.0 TB onto a 2.5. Jp magazine did that a few years ago and felt if anything, it actually lost a little power afterwards but certainly no noticeable improvement. Besides, opening up the intake ONLY helps at near redline rpms at wide-open throttle, not how many of us drive our TJs. As opposed to many car engines that are, none of the TJ engines have restrictive intakes or are starved for air.
That reminds me of a bad interlock switch, like the clutch or neutral safety switch if you have an automatic. If you have an automatic, try moving the shifter back & forth over neutral to see if it will start. If you have a manual, try inserting the fuse into the clutch interlock bypass location described in the owner's manual.