It will take some work, but it's perfectly doable.
Enemies with special defenses
The players won't have access to see invisible, flight, magic weapons, or ghost touch. Therefore, if you include enemies that can fly, or have DR/magic, or are intangible, these will be huge challenges, and may be downright impossible. The easy solution is simply to not include such enemies, but the more interesting way is to treat them as nigh-invulnerable enemies that the heroes will have to figure out how to defeat. In a normal Pathfinder game, a ghost is a normal critter with a +2 CR template pasted on top, and requires some minimal preparation to defeat. In a low-magic Pathfinder game, a ghost is a mystery: why did they become a ghost? How can you persuade them to pass on, or at least let the party pass by peacefully? Can you persuade the local priest to perform an exorcism, and will it even work? Instead of "find monster, insert fireball," these types of encounters are now role-playing challenges, because they can't be solved any other way!
Alternatively, you can simply strip out the special defenses from enemies. Pathfinder assumes you have level-appropriate counters to special abilities anyway, so by removing those special defenses, you aren't going too far from the original intent. Adjusting the CR is left as an exercise for the GM, because it's going to take a fair amount of trial-and-error to determine what the right balance is.
Fixing armor class, and other numbers issues
Pathfinder assumes that both attack bonuses and defenses will be augmented by magic items. This partially balances out if the players don't have magic items, but consider giving everyone a +1 bonus to AC and all defenses every four levels. Don't make them pay a feat for it, just give it to them.
While you're at it, give your players bonus XP for the monsters they defeat, by calculating the XP as if the monsters were a higher CR. Since they're operating without magic, every encounter is going to be harder than what the DMG "expects" when it calculates XP per CR.
What will they do with their money?
Your players won't be able to buy gear that personally enhances their ability to make things dead faster, or grant them new solutions. If you keep to the normal loot rules, then the party will have far, far more money than they know what to do with. You have two options here: give them less money, or give them something to do with that money.
Let them invest in mercenary companies or land holdings. Let them become influential in the church, or their hometown, or even their country as their economic might and donations in the right places give them power that they would never be able to take with a sword. Favors in high places give characters some very powerful options.
Recovery after combat
This will require explicit house rules; you'll need to accelerate natural healing (heal a percentage of HP per day instead of a flat amount?), allow Heal checks to do much more than they normally do, grant the local clergy some extremely localized healing powers (they can heal people brought to their church, but not outside of their place of worship), and/or make this a political game rather than a hack-and-slash game.
If everyone's having fun, then it's a good game. It doesn't matter if the characters aren't optimized: as long as they feel like they're making a difference in the world and they're enjoying the game, then you're doing it right. The characters will be balanced, more or less: they all don't have access to magic, so intra-party balance isn't as much of a problem. You'll see that the players lack all of the magic-based solutions that you'd expect in a normal Pathfinder game, and you'll select the enemies more carefully, but things will work out fine. Let your players know that things will be a bit different than normal, and your players will go along with it; they requested this kind of game, after all.
Beastmaster is a bit of a trap
The Hunter Archetype incorporates both the Hordebreaker and Giantslayer archetypes from the playtest into itself, letting players pick and choose their features as they level. Either way you build is a strong choice and the Hunter gets Volley or Whirlwind at lvl 11 which really ups their ability to deal damage to multiple targets in a round. In comparison the Beast Master is only getting a CR 1/4 ally which costs an action to attack. You are able to make 1 weapon attack yourself when your beast attacks at lvl 5 so at least you aren't missing out on the extra attack, but this will scale very poorly as you always only have a CR 1/4 beast as your companion. Even though the Beast eventually gets to make two attacks itself, and gains the benefit of any spells targeted at you as buffs it still is a very, very poor choice in comparison to the Hunter's abilities. Also, why would you ever want to be like Drizzt?
Ranger spell-casting is utility focused, not inherently weaker
Rangers get a lot of healing spells in their list and share them with clerics. In addition to that, Rangers have access to a lot of buffing or debuffing spells with which to help the party and impede their foes. Additionally, they have some very strong story and skill oriented spells allowing them to track and find objects and people and manipulate nature to their advantage. This synergies with the class features the core Ranger gets with their Natural Explorer and Favored enemy features.
Rangers are still a strong choice — they just aren't as purely combat oriented as they have been in previous editions
Rangers in 4e were the striker with twin-strike at level one and a plethora of nova-round dailies and encounter powers. 5e's Rangers, while very competent in combat, are designed as a class to be tied to a certain type of terrain(s) and enemy type requiring some work and buy-in from the GM and the table to reach their peak effectiveness. From a flavor perspective, the ranger is closer to the Rangers in Tolkien's works.
Like Faramir, Aragorn or even Legolas, the ranger is extremely competent in his terrain of expertise and hunting their favored enemies. In terms of a campaign, the ranger could make all the difference between barely surviving and constantly being beset by monsters while traveling the wilderness and actually thriving, ambushing enemies first, avoiding them at will, and always being able to find and forage food to keep moving.
Best Answer
The default D&D combat flow is not intended to do what you are trying to do; it works really well when pitting two roughly equal groups of three-to-six hostiles against each other, but too many or too few on either side lead to drawn out or static encounters respectively. In encounters I've run where a PC is scouting alone, I've found that it really runs best when not run any different than any non-combat encounter, save for the fact that you're using weapon proficiency and armor classes instead of skill proficiencies and difficulty classes. This also frees you to run a scene that is more dynamic than a straight up murderfest.
As far as what kind of enemies, the default assumption of D&D is that the PC's are supposed to win, so make sure that they're weak individually (CR1/8 or CR0 for the levels you're talking about), but you can make them plentiful and/or give them abilities that will not necessarily kill the players, but will impose conditions that will make it that much harder to achieve the ultimate goal. This encourages strategies for the lone PC to pick them off, one by one, Batman style, and use distractions to clear the way. However, if they get reckless, you can still punish them by having a large number of enemies converge on them, thus keeping the perceived threat high. You may even want to sprinkle some singular CR1/4 enemies in there as well, but warn the player that if you make too much noise taking them down, others could come to their aid. Depending on what kinds of enemies you're facing and the story you're trying to tell, bribery and deception could also be tools the player could use.
Example similar to a game I ran:
In summary: Use individually weak enemies, in large numbers, but spread out a bit, and make it clear that they will aid each other if the player attacks recklessly; leave props, options, and landscape open to allow improvising players to set the fights up to favor them or to avoid them altogether; put decision points at places that will allow them to avoid combat if they so choose; and don't be afraid to set combat rules aside for the sake of a more narrative approach.