I have no clue what to do about this

Your 4x4 manual has a 0.81 5th gear. Paired with a theoretical 3.31 axle gives you 2.68 overall ratio.
The 4x2 automatic has a 0.71 4th gear and 3.58 axle, giving an overall ratio of 2.54.

The 4x2 automatic has taller gearing (lower rpms on the highway), skinnier tires, lower ride height, 400 lb less weight, and gets only 25 mpg EPA highway.

This means, with a 3.31 gear swap, you will get 23-24 mpg at best.

 

You don't want steeper gears with a MT transmission. I had an 08 4x4 MT that was atrocious. I think they put the wrong gears in it. They were way to "steep" IE: I had to ride the clutch a little to get it going. Think what happens if you are on a hill trying to start out and have steeper gears. You will have to ride the clutch. Same for towing. Trucks should have a nice low 1st gear. Your truck is perfect!

 

A steeper ratio will just lug the motor down. All of the Toyota trucks I have owned never really got good fuel economy, the best being my 88 4Runner with a 22RE, which got just slightly better than my 06 V6 4wd.

Its too bad you guys in the states can't import diesel vehicles from Japan, Im thinking about picking up a 90's Hilux double cab, 3.0L 1KZTE 5spd with a solid front axle! It will cost me about $20,000 said and done, some sell for closer to 10k.