End of civilization is generally quite a bit higher level than 5, but thats not so important. :)
Your idea is fine. Its an outline with no problems. The hard part will be filling in the details and making sure your players keep on having fun. You'll need combats/obstacles/puzzles that will challenge your players with out killing them off. For them to have fun, you'll need to keep it varied and make sure everyone has a chance it do well.
There is one potential risk with your idea, and I will have to generalize because I don't know you or your play style. Something that can happen with new game masters is that he or she will have a grandiose idea for a campaign and pour his or her heart and soul into it. Players have their own ideas and things don't always run according to the GM's plan. Sometimes at this point a GM will "railroad" the group into staying on course, and this is considered a bad thing, as you are forcing the group to stay in the story you have written. Remember that you create the world, but the players are improvisational actors in it. A problem should have more than one way to be solved. Failing at a single effort or not finding one clue should never bring the game to a grinding halt. The players will see your world differently than you do, so you must remain loose and remind yourself to not become too attached to your own story. Sometimes a PC gets lucky and kills your cool villain in a single attack. Let them enjoy the victory and move on. Maybe you'll learn something. Don't keep the villain alive until he gets a chance to do the cool thing you designed.
Sorry for rambling.
I second Ciaran in that a GM needs to following the golden rule of improvisation, "build on what the other person puts forth rather than tearing it down." If a player wants to explore somewhere or do something, let them. You might have to think on the fly (which is why knowing where the right mechanics are can be important). If all else fails and you can't find the mechanics for a given situation, wing it. Use your best judgement and always, always, err on the side of the players and them having fun.
Unless your players are jerks. Then screw them.
Your adventure seems pretty straight forward and should mesh well with the mechanics. Sometimes it is okay to fudge the hit points for your bad guys, not necessarily so they can do something cool but sometimes a player who doesn't always get to shine needs a win by landing that final desperate blow. Sure, the fighter may have technically killed the big bad evil guy on his turn (like every turn), but if one of the other players fell flat on their face earlier, they might have the chance to redeem themselves in the battle with a decisive strike.
As always, depends on you and how you want to play the game.
A lot of great advice so far.
Read, read, read. Know the rules so you can help your players stay on track, there are a lot of books and a lot of rules so this will take time, PF books also have nice information of class ideologies, religions, organizations, etc that can help build flavour. Paizo and D20 have most of the material online for easy access.
Set the rules of your table and stick to them, if you are going to introduce house rulings make sure everyone knows it before hand (or there is consensus on the fly) and that chance is recorded for future use. If you are only using certain material, make sure everyone or no one uses it, it is no fair if one person has access to more spells or different equipment than everyone else.
Make sure your players know what the game is going to be about (it is no fair if someone makes a character that cannot use most of its abilities ie crafting wizard where crafting is banned).
The number of players and their classes can have a big impact on gameplay, the more players there are, the more damage they can land on a single foe before it can respond, at low levels this is less of an issue but can quickly spiral out of control when everyone has 3-4 attacks, plus animals plus summons etc. I find (running a 6 player game) that more smaller enemies is better than a few big bosses (I try to mix tough and tiny).
I roll 2D20's, I feel dice fudging should be limited to extreme circumstances, but 2 D20s generally means one will be what you hoped to get (if they are both low then so be it, or if 2 nat 20's means a player dies, then it was in the dice and the players won't feel that you are being vengeful [I try to roll potential death strikes in the open]).
Have some backup baddies ready incase your players take an unexpected dive into a cavern you thought was unimportant. You don't need much, some loot, some baddies, a basic description and flavour items (strange loot, decorations, clues to the inhabitants living their lives), and a basic layout, but finding the stats or calculating decent loot can take time. A slow player can be fixed (or delayed action), a slow GM means the game stops.
Your players will go off track, be ready with some names, some stats, and improvisation. Reward them for exploration, but make the story MORE rewarding so they are inclined to stay on path. Lists at hand can be really helpful.
Have ways of getting back on track. Maybe they skip the room with the informant, or disintigrate the man with the note on him, or fail their perception for that secret door. It happens often and a good GM will have a second option that the players can find themselves without too much GM interference, when all else fails a friendly NPC can always make suggestions or ask poignant questions.
Flavour your "loot" art or expensive dishes, or gemstones are worth the same but can make a pile of loot seem more interesting (and dungeon appropriate).
Make certain your players are prepared for what they are going to face, at low levels saves are not good, damage is low, and health and AC are low. Things like DR and SR can cripple a party without appropriate spells or gear, know what they have and adjust as necessary either with different monsters or appropriate gear/scrolls as loot.
Grab a boogie board or a dry erase board so you can publicly display initiative, ongoing effects, etc. The game flows better if everyone knows when they are up next or need to roll a save (delayed actions and large parties can make initiative hard to track sometimes).
2 tips:
Find a nice font (edwardian would do)
Print a note, tear of the edges and soak it in black tea. Makes it look like parchment.
Buy some fake brown leather, cut some circles in it. Make tiny holes on the sides for a chord. Makes nice dice bags.
Also now what the characters classes can do, assuming the players are new.
That way you can help a player who feels like a 5th weel.
There is no right or wrong way to have fun when roleplaying, as long as everyone involved is having fun.
A slightly more advanced technique for GMing is to plan situations, not adventures. I decide what the bad guys are going to do, assuming no interference from the PCs. It is entirely the PCs' choice how they interact/interfere, based upon what they learn/discover. The NPCs then have to react to this change in circumstance. It requires a bit more work between sessions (especially when the PCs completely derail the plotline), but really helps avoid railroading.
Also: learn to count to 3 (see my previous post)
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I'd advise you to spend some time thinking of tangents and unrelated plots. So you're starting in Varisia, Sandpoint I assume, and that could include a trip to Magnimar. Start getting an idea in your head of what that would look like now, and even flesh out some basic plot points for such a trip. That way when a player up and decides to go to town, you flip through your notes and/or mental file drawer and pull those ideas out.
Also, be prepared to 'file the serial numbers off'. Say they don't go to Magnimar, but some other city instead. Use as many of those same plot points as you can, just reskin them to fit the new city.
Anything you can think of around the area that might be even remotely related probably deserves a line in your notebook. And who knows, you might wind up inventing something you really like that you can reskin back into the main plot.
Finally, as new GM advice goes, don't be afraid to ask your players for mercy. E.g.
"Guys, I don't have anything planned for your idea, but it does sound really cool. I can have something prepared for next week, but can we stay on track tonight?" And if they say 'no' be prepared to bust out the Munchkin cards or do some other group activity.
1 thing i really did wrong was building combat statblocks for npc's instead of writing down their personal details. You can give sheriff hemlock archetypes, feats and a prestige class, but combat npc's if not really necessary just slow things down. If you just right down he walks around shirtless drinking beer, has a huge air and gossips about villagers (or something like that) that will help you far more to set the scene and develop a realistic world.