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.
The rules for creating custom magic items are in the Dungeon Master's Guide, table 7-33 and nearby pages.
On page 288, under the Adding New Abilities header, are the rules you need for adding (you guessed it) new abilities to existing magic items.
A Wild armor/shield (Racede of Stone) is subsumed into your new form but the armor/shield bonus stays. It can be used in conjunction with a tunic, so you don't go around naked. My MoMF used to drop a big blanket on the ground before morphing into some giant form, using it as a peplum. Unless you need to morph during battle, I found it to be an ok way to manage nudity.
As an alternative, Beastskin Armor (MIC, p. 7) uses wildshape charges to change shape with you. MoMF gains lots of WS uses, so the solution is viable as long as you don't change shape too often.
Best Answer
Magic items are more interesting when they serve to advance or drive a plot. This may be because
Only with that item can the characters succeed (and it is hard to get or keep the item). Example: wights that can only be hurt by +1 weapons, in an area where +1 weapons are extremely rare.
The item is complex; it only sometimes works, or requires mastery and exploration. Example: a Wand of the Moon which has greater effects at night than during the day, but the nature of the effects change with the phase of the moon (all of which the characters have to find out).
The item has a long and elaborate history, some of which is relevant to some grand plot or event. Example: a horcrux.
The item is unique, and even if not all that powerful, the characters become known as the ones with that unique capability, if only they can make it. Example: the characters have to create +1 swords for wight-slaying, and they learn from an old magician how to both enchant the swords and make them glow if wights are within 100m.
You cannot, in general, make people super-excited about items that are commonplace and easy to get, no matter how fantastic they are. For example, in a matter of seconds, I can talk to any person I choose on the planet, thanks to a cell phone. Do I spend much time thinking about the cell phone itself? Not really. (Apple does a good job at making its products seem extraordinary, so if I had an iPhone it might be a partial exception.)