I think they are making it meet EPA 2007 or 2010 or something. So what that means is you can use it to repower any on-road vehicle built before 2007 or 2010.
The EPA rules state that you can repower a vehicle with the same year model engine OR newer. So that is what they are going for. I don't know if they'll go for making it EPA 2017 complaint.
The one I saw in the ~2000 TJ, it looked like it had only a DOC on the exhaust. If so, then that would be good.
This is a common rail injection engine. From what was said on Dirt Everyday's episode, I think it is a Bosch system. So with that, the DOC, and EGR, it'll require ULSD to operate. So yes, full mechanical engine and the latest high pressure equipment.
The 2.8 vs. the 3.8, from the specs I saw, the 3.8 won't have much more HP, but has an extra 100 lb/ft of torque. I guess that is good, but for our light applications I think the 2.8 would be better. Smaller, lighter, and uses common cheap transmissions. I don't know what transmission you'd need to run the 3.8, but probably a NV4500 or something.