I swapped on some Aisin manual hubs. I have a 1999 with 16" wheels. The center caps from 95 Trooper wheels with hub cutouts fit fine and look stock. The hubs come stock on 88-91 4cyl auto Troopers and on 89-94 Amigos.
I've hit the TOD button while unlocked by mistake once. It didn't do any more harm than running in a normal 4x4 with the hubs unlocked and the front axle in 4-high.
I haven't done any kind of conclusive mileage test. Best I can say is 1mpg seems right, but there could have been other factors. If I had time to spend an afternoon messing around on the same stretch of road I'd have a better answer for you.
In any kind of wet weather I have them locked though. It's easy to get a bit too much throttle and end up spinning the rear tires, which isn't much fun on the corners.
-Tad