Gears would be the thing that could get most "performance" out of it without touching the engine. I never touched anything on the engine on really any of my trucks, but going from 3.55 to 4.10 on the D2 and 3.73 to 4.88 on the TJ made a worlds of difference. I haven't found myself needing 4.56s or 4.88s on the Raptor, but it doesn't mean I haven't thought about it.
I know its not a performance mod, but I think upgrading the transfer case skid plate it super important.
Complete the underbody protection of your 2009-Present F-150 with an RCI Metalworks transfer-case skid plate. Protects the vulnerable and low hanging transfer-case from on and off-road hazards
rcimetalworks.com