So I want to make a zombie character...

[Patryn of Elvenshae]

Looking at the Gravetouched Ghoul, it mentions their claw/claw/bite under a header "Full Attack". There is also text mentioning that if they have a weapon, they choose the claw/claw/bite or weapon. That leads me to believe that it's a full attack option, which normally don't just add onto other attacks, like flurry of blows.

It probably says something like, "Full Attack: 2 Claws +X (XdX+X), Bite +X, (XdX+X); or by weapon."

There are specific rules that detail the interaction of mixing "manufactured" weapons (like swords and unarmed strikes) with "natural" weapons (like claws and bites).

The rules state that you can mix them, but all natural weapons are treated as secondary (and so have a penalty on attack rolls and apply less of your Str bonus to damage).

If you want to read them yourself, you can find them here: http://www.wizards.com/d20/files/v35/TypesSubtypesAbilities.rtf

 

[IcyCool]

Looking at the Gravetouched Ghoul, it mentions their claw/claw/bite under a header "Full Attack". There is also text mentioning that if they have a weapon, they choose the claw/claw/bite or weapon. That leads me to believe that it's a full attack option, which normally don't just add onto other attacks, like flurry of blows.

Your claw and bite attacks are natural attacks, and follow the natural attack rules. Unless you are using the full attack option, you only get one attack.

Now victims hit by the Claw or Bite attacks inflict Paralysis. A Monk can attack with any body part, which I'd assume would include claws/nails (if the race has them) and bites. Is there a ruling that would prevent Paralysis & Ghoul Fevor from working with Flurry of Blows if the attack is described as being from the claws/bite?

No, you only inflict paralysis and ghoul fever from your claw or bite attacks, not your unarmed strikes.

Being a Ghoul, I'm pretty sure being Lawful is right out. Under the undead class of ghoul it mentions that Ghouls are CE and how to 'relax' that for PCs. Lawful is described as exceedingly rare and while I don't want to be evil, I'm going to be a flesh eater and very conflicted so I don't want to be lawful.

Then don't go Monk, go Rogue. You get sneak attack, and three attacks a round in a full attack (Claw, Claw, Bite). You could take a few levels of fighter to up your claw and bite attack power with feats.

Aside from taking up Fighter with a focus on unarmed combat afterwards, is there another class (or PrC) that deals with unarmed combat that wouldn't conflict with many levels of Monk? Or even a variant Monk class for the "non-lawful". I'm limited to D&D books, not other d20 stuff.

Nope, Monks don't really have a whole lot of options as far as that goes.