I built a $46,015 FX4 4x4 157" WB and a $45,970 Lariat 4x4 157" WB ($85 difference) using your criteria listed and from what I can recall, here are the differences:
1) The EB is an $750 option on both trim levels.
2) Leather is standard on Lariat, optional on FX4 as part of Luxury Pkg. The Lariat buckets are heated and cooled, the FX4 is heated only.
3) Center console (Captains Chairs) are optional on Lariat, standard on FX4.
4) Max Tow - optional on both trims but axle is Limited Slip on Lariat and ELD on FX4.
5) Nav/Moonroof - optional on both trims, part of FX Premium Pkg.
6) 18" wheels are standard on both trims.
How did you come up with a $1k difference? I may have missed something during the build on www.ford.com