How about handing it sorta like potions? Have a stunt which is supposed to reflect modified weapons, which gives 1 ( or maybe 2) modified slots, so to say. You can do 1 of 2 things with these slots: 1. either declare at the beginning of the mission what kind of mod you have, e.g. maybe silver bullets, laser-sights, or a night-vision scope. OR you could leave it empty, and by spending a Fate point you can declare what kind of mod you have e.g. so you say we are surrounded by monsters on all sides? My assault rifle has has an extended clip which gives +2 to my weapons roll when using spray attack, take that!! Or something similar.
