I think you should consider starting over.
The only stat that really matters is INT. You should always start with 9. The INT bobblehead is the only reason you don't push it all the way to 10. Your skills will increase much faster, and skills are everything in this game.
STR, END, and CHA can stay at 5. Go with 6s for PER, AGI, and LUCK so you meet the prereqs for some very enticing perks. If you run out of points, spend your spare perks on Intense Training for additional stats.
For skills, go with repair, small guns, and lock picking. Small guns are by far the most common early on, so you'll be able to keep your weapons in great condition - and condition dramatically impacts damage output. Lock picking will grant you access to tons of additional ammo and gear as well.
If you can help it, don't spend perks on "skill increasers" like Gun Nut. With a high INT, you should be maxing your primary skills right about the time you hit level 20. You're better off spending perks on bonuses that help you survive in combat. Anything that increases your damage output or improves your damage reduction/avoidance should be a priority.
Finally, make sure you fully exhaust the quests in Megaton before you embark on the main story quests. You'll grab a ton of skills, perks, gear, and combat experience finishing off the various side quests, all of which should make your treks into downtown more bearable. Moira's survival quest to the supermarket should outfit you with absolutely everything you need to, well, mow down raiders, ghouls, and super mutants.
Oh, and shoot super mutants in the head with the combat shotgun at close range. That really solves their whole "having a head" problem.