Rule number 1: This is your world. Your rule. If you think that firearms would be common to the point of like, even the commoner protects his farm with a shotgun, hey..go for it!
Just keep in mind that you would have to make the guns Martial weapon instead of requiring a specific feat. So that any military-grade training will provide training with guns. Or maybe even simple weapon (depending if you use gunpowder or alchemical shells). Because it's not that hard to pull a trigger and point a certain direction.
Guns are really powerful in Pathfinder. I noticed that when I had two gunslingers at my table. I would throw them monsters with damage reduction and lots of touch AC..because your player will shoot and kill everything at range.
Also, if guns are that common, players shouldn't feel like they are the only guys in town with them right? If everyone has guns, even the goblins ambushing them on the road will be a really interesting encounter.
For feats, most characters get a feat at first level, and then another feat at every odd-numbered level. Humans get an additional feat at first level. So, your example 5th level Elf will have 3 feats available. If you have a WOW background, think of feats as talent points - they let you customise your character a little more every couple of levels. This is spelled out in the table on p30 of the Core rulebook.
The bottom of p27 of the Advanced Player's Guide (APG) outlines how many formulae are in your book by default - at first level, you get 2 1st level, plus an extra first level for each Int modifier. At each level after first, you get another 2 formulae of any level you create. So, by 5th level, you would have 10 plus Int modifier formulae, of which up to 4 could be 2nd level formulae.
You can also use bonus elixirs each day based on your Intelligence, so you'll likely get an extra one of each level, but check the bonus spells table in the Core rulebook to be sure (not sure what your Int is).
Elixirs are totally separate to bombs, even though the rulebook confuses things by mentioning them both in the 'Alchemy' rule. The Bomb rule on p28 of the APG, halfway through first paragraph, says you can use a number of bombs per day equal to class level + Intelligence modifier.
The Brew Potion feat allows you to create a potion version of any spell in your formuale book. Think of it as making a lasting version of an extract. This is described on p551 of the Core Rulebook. You can also make alchemical items (i.e. Alchemist's Fire, acid etc), and the rules for this are covered in the Skills chapter, p.91. The items you can actually make are in the equipment chapters of the various rulebooks.
Good luck, and have fun with the alchemist.
Best Answer
It seems to me that your question is two fold. I may be wrong but you seem to be looking not only for a technical point of view but also from a role-play point of you.
The technical aspect is quite easy to answer:
You will need two items to produce your concoctions(extracts, mutagens and bombs):
The second item is your
Extract's preparation How to make an extract. Most of the text around extract can be reduced to the funny (or not) "spell in a bottle".
Alchemist extract are like spell really but with a kick they don't take as long to prepare, unless you have more than 60 extracts and at this point well... breaking action economy should not be too hard. The downside is that you need to redo it every day so no storing for long winter nights!
Mutagen's preparation
Now comes the preparation aspect on how to make Mutagens. As far as I can tell, the usual in D&d is to be quite abstract and left to the imagination of the player the details. Most of the time for spell caster you have to go into splat book and descriptions to get a "look and feel" and not only the "use a standard action".
Emphasize mine... A mutagen is brewed, so it is likely to be prepared like a potion or extract but being far more potent it takes a whole hour to make one dose and the alchemist aura can only "power up" one at a time.
From the Alchemy crafting Kit, we know that you have all you need is in it.
So you now have the physical elements and you know that it takes you an hour to brew it.
I hope this will be sufficient for you to feel comfortable using your mutagen.