I've played with making Fallout-esque things in different systems/settings before, it's pretty fun to do. Going point by point from the Shadowrun system, though...
1. You'd need to flesh out mutation and a new version of Radiation rules, that's for sure.
2. Ditching magic is simple enough.
3. Having limited Matrix stuff for when you can access old computers (make it possible to reconfigure those Sentry Bots and laser death fences) seems like the right idea.
4. Figuring out the effects of various drugs wouldn't be too hard, nor would statting out the various weapons/armor/gear you come across, but;
5. Figuring out a good mechanic for quality and degradation over time/use would be more important to work up.
6. Prices for various things will need to come up, as well as throwing out the majority of the cyber and bioware (there's limited stuff, but it is a post-apocalyptic setting; getting it/a source would be a campaign of its own in my opinion).
7. Making a character creation system without the Races in it might be necessary, unless you can come up with enough options besides humans, ghouls and androids (maaaybe Super Mutants as your 'trolls').
8. Writing up all the dangerous critters.
9. Perhaps shrinking down the Attributes to match the SPECIAL of Fallout; Strength (Strength), Perception (Perception), Endurance (Body/Willpower), Charisma (Charisma), Intelligence (Logic/Intuition), Agility (Agility/Reaction), Luck (Edge). That's quite optional.
10. Definitely implement some proper weights and a carry capacity for people, because the survival roots are important; Ammo needs a weight too to make those Wanderers pack carefully.
11. Flesh out the Street Cred and Infamy system so you can make a proper Reputation chart/system; who's friends with who is important.
12. Perks are extremely important; treat them a bit like Martial Arts/Positive Qualities.
13. There's also Karma to consider; adjusting Perk availability to some extent would be a good way of representing that. The Cannibal Perk shouldn't really be out there for the paragons of kindness and dignity, for example.