Keeping the lift with 31" tires really isnt gonna get you any more clearance, as the only thing that will lift your differentials up in the air is larger tires, and they WILL get hung up on rocks, among other things. lose the body lift at least, the only point of lift is to fit larger tires, and unless you do a drivetrain lift the body lift does nothing. The best suspension mod for IFS is BJ spacers , its the only thing other than really expensive long travel kits that will get you more susp. travel. Gearing is important. even with a 2nd transfer, you will have both in 2HI 90% of the time, during on road, fire road, anything but rockcrawling or climbing. i used to think my gears were fine (4.10 with 31's) then i switched to 4.56 and it made a huge difference across the board.
Throttle body: my opinion unless your truck is turbo'd, dont waste your money. for towing power you want to keep as much low end torque as possible, put in the engnbldr 261C cam, and i used an adjustable cam gear from LC engineering and advanced my cam timing 3 degrees. if you can afford is, go back to 2.25 exhaust, itll make a difference.

just my 10 cents. good luck!