You are over-thinking the situation, don't worry about the 5spds having an overdrive, the 5spd's 4th gear is 1:1 just the same as your setup in Drive.
Stock tires are not 29", at the most they're sometimes 28" unless the jeep came with the 30" tire package (and I believe that option was most common with the 4.0L engine). Most 4bangers will be 27" or 28" I believe.
3200 is not screaming for the 2.5L, it's very happy in that range. 3200 is screaming for the 4.0L engine.