You have to watch your progress in game. Check that you saving before level 8, 14, 20 so you can level up with all Karma trophies then you can reload and go for what ever Karma you want. Before I hit level 8,14,20 I would save then go to megaton and steel and Save then kill or steel to get my karma neutral and bad once I got the level up I would reload go for next. Once you get them out of the way your all set to grind the rest of the mission trophies. I suggest if you want to play as good karma you make a save for doing Strictly Business. I would also suggest you save before you do You Gotta Shoot 'Em in the Head so that you can keep keys and get T-50 power amour in Fort Constantine. As for the Nuka Cola Challenge I l collect nuka colas until I am high enough level for the Quantum Chemist perk (Broken Steel DLC Needed). Save all them Nuka Colas put them in a container and for every 10 Nuka Colas you get one Quantum so put them with the other Quantum's you found along the way and you set, You should have your house in Megaton by now I would collect stuff for making weapons along you journey and stash in your house and when you hit level 26 you unlock Warmonger Perk and unlock all weapon schematics.
If you have any questions ask me on PSN gene2004.
I put Youtube links for the trophies for Bobble head locations and Super Mutant Behemoth Locations.
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http://'www.youtube.com/watch?v=BfYHcjp5gm4'
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http://'www.youtube.com/watch?v=nyPU9vhfuqI'