I would recommend using the Monster Vault maths, found summarized on Blog of Holding; or, Monster Maker is a handy app that helps create monster cards, and will work out the maths if desired.
Set out which roles you wish the monsters to take - from the sounds of things it seems like you'll have a mix of Lurkers and Skirmishers, with Soldiers and Brutes making up the majority of the rest. Adding some of the other roles (artillery and controller) will help build variety.
Essentially you will be making sets of 'monsters' to form into encounters. From memory approximately the same number of same-level enemies makes a relatively balanced encounter, depending on the level of optimization and experience of the players. Mix and match some monster types, replacing 1 monster with 4 minions of the same level, and nudge up or down to taste.
For example, for 5 level 1 PCs you could then have 2 'Tough Monks' (level 1 Soldiers), 2 Ninja (level 1 Lurker), 4 mook monks (level 1 skirmisher minions) and 4 ninja mooks (4 level 1 artillery minions).
The DMG 2 has a section on making monster 'themes' - in essence by putting together sets of additional abilities that are thematically linked - such as the Goblins' ability to shift. For instance, you could add an ability to the Monks that acts in a manner similar to the Monk PCs flurry of blows - maybe on a successful attack they deal a small amount of damage to an additional adjacent enemy, maybe 2 damage for a level 1 monster.
One of the easiest tricks for 4e is to simply 'reskin' a monster - presenting for example, a goblin or a kobold as a ninja is just a question of description. Find a monster which has the relevant ability (such as shifting on a miss, those pesky goblins!) and you're good to go.
Generally a 4e encounter is much better with some environmental factors, so I'd recommend adding in some interesting terrain features or traps to spice things up a little. Broadly speaking, avoid adding in higher level Soldiers or Brutes too much, because they can become hard to hit leading encounters to bog down. Lots of minions is useful in making an encounter feel exciting and allowing the PCs to feel capable heroes - it all comes down to description when using minions - you can make the heroes feel awesome or like they wasted their attack depending on how you invoke their sense of adventure.
The monks could have the ability to spread some splash damage as a flurry of blows, the ninja should be tricky to pin down, maybe with a teleport style ability or a jump. They could climb walls with normal movement for a more HK film feel. The tattoos sound like a great idea, possibly you could borrow from Legend of the 5 Rings and each style of tattoo grants an ability - so the monks with flame or dragon tattoos can breath fire. Monsters that spawn other monsters are fairly tough - the Wraith in 4e does something similar I think. Make sure that whatever comes afterwards can't spawn more monsters - maybe it generates a minion when killed that lacks the respawn ability. Alternatively, you could describe them as crumbling and rising once they hit Bloodied, with some new abilities?
(Background: I am also a Christian, along with several of the people in my gaming group.)
tl;dr -- The fictional god of your fictional world is not the God of our universe. Make the fictional god clearly distinct from our God. Figure out how much of what the party knows about that god is true.
Define what you mean by "God" in your game world.
Your game world is a fictional creation. The God character in your fictional world is also a fictional creation. He (let's call him Steve) is not the God of our universe.
So if Steve isn't our God, in what way is he the god of your game world?
- Is Steve all-knowing or merely mostly-knowing?
- Is Steve all-powerful or merely mostly-powerful?
- Does Steve have a physical location in the world or is he everywhere at once?
- Did Steve create the world or did he pick it up later on?
- Does Steve intervene in the workings of the world or is he an absentee landlord (perhaps only stepping in at the end of the world)?
Characterize the god of your game world.
The God of our universe has some very particular characteristics. Steve could be the all-knowing, all-powerful creator of the universe, and yet not be much like our God. Christianity describes a God with some very particular characteristics, a God who loves his creation, is triune in nature, is slow to anger, steps into the universe as a human, finds the aroma of burnt offerings pleasing, etc. There's no reason Steve needs to have these particular characteristics. Imagine that Steve has characteristics of his own:
- Steve always appears as five figures at once. Each one embodies a different aspect of his personality. The dragon speaks about wisdom and long-term plans. The butterfly whispers about transient beauty. The giant speaks about using power to achieve results. The coyote speaks about relationships with others. The child speaks about the deep things of the listener's heart.
- Steve wants his followers to gather in the open air on hilltops when they conduct their worship of him. His people have come up with several reasons why they believe this to be the case -- some of them are correct, some are not, but Steve always has many reasons for doing what he does, most of which are beyond human understanding.
- Steve deliberately established five separate churches in the world, not just one. The five churches each have different areas of interest and responsibility, different tasks to accomplish in the world. These churches (being made of mere mortals) have very little comprehension of Steve's great plans for the world. Sometimes they think they're working together and sometimes they think they're working against each other, but it's all part of Steve's unknowable plans.
- Steve is not concerned with whether people believe in him or not. Belief is not required for salvation, because...
- Steve brings neither salvation nor damnation to people. We live, we die, then we live on in our descendants in a literal way. Each of us is a composite of all of our ancestors' souls, plus a unique spark of our own. When we die, we become part of all of our descendants. Steve has a special plan for those who die childless.
Match Steve to your game world.
It's been three years, and you've probably established many expectations about the god of your game world. Figure out what the players know for sure and make up your own Steve that fits with that knowledge. For example, if you've presented the party a vaguely-Christian world:
- Steve is believed to be a triune being -- because two of Steve's five aspects are not understood by the people of this part of the world.
- Steve is worshipped indoors at a temple like the temple of Jerusalem -- because people understood the instruction to worship on the temple mount, but they added the idea of building over it later, borrowing from pagan religions around them.
- Steve is believed to judge everyone when they die -- but everyone is made of all the souls of their ancestors; at the end of the world the evil souls will be filtered out and the good ones persist.
Best Answer
Well, this is a great question, and I must say beforehand that my experience with an organization of villains is pretty narrow. But I do hope that what I'll write here might be of some use to you.
Inspiration
One of the key things that you can do is to find inspiration for your villains in other sources. I once based an organization of villains around the 7 exes from Scott Pilgrim vs the World. Another time it was around a bunch of villains from westerns. The trick is to find some villains that are cool and draw inspiration from them.
This inspiration can be in terms of copying the villains, or it can be in terms of taking certain parts of their personalities. It can even mean analyzing what made them so memorable and using that someway.
Make them somewhat related to the characters
You want your players to care for them, to remember them, or something around those lines. For that, you have to make them related somehow to the PCs. While having them compete for the same goal is nice, I do prefer something closer to the trick utilized in Scott Pilgrim, having them the exes of a certain friend, relative or the like. Maybe have some of them be immediate family of the PCs? A true connection is far better in order to make the players care for them enough to hate them, love them, or even love to hate them.
Make each one of them unique
This is also very important. While they are all a part of an evil organization, they must be unique by themselves. Each and every one of them is also a villain that the party will have to encounter one day or the other. In Hot Fuzz each one of the conspiracy members is unique and is colorful enough to be remembered. We have the couple who hate the reporter for stating the wife's age is higher than it really is. We have the farmer whose mother has a rifle. We have the chief of police who doesn't punish criminals and we have the manager of the Supermarket who is always there when you least expect him. In Scott Pilgrim we have the Female ex who Ramone experimented with, we have the actor who has doubles, we have the leader who is an agent and who can control Ramona and so many more.
Go for it too, make them unique, make them colorful, make them come alive as persons and not only is a part of an organization. The fact The Joker fights sometimes alongside with Bane doesn't make each one of 'em less frightening, unique or evil, right? Why should that be the case here?
Have something common for all of them
Being unique doesn't mean that they have to be completely different. In Scott each of the exes is an ex of Ramona, and an idiot. In Angel they are all attorneys. In the first and second seasons of Buffy they're all vamps. Have something that unites the villains that is common to all of them. Maybe all of them have similar clothes or use the same perfume? Maybe they all talk a bit funny?
As a bonus, if you can make the uniting thing a thing that is cool and all by itself, which can make alone the villain stand out, it is even better.
Let the players know of them in advance
The characters should know about the organization pretty early, but having the players know about the organization even earlier can do magic sometimes to your campaign. If they'll know that their characters will fight an organization of villains, the players will look for them (and with far greater anticipation). Always remember that the players are authors as well as audience, and if they will be looking forward to meeting the villains they will far better enjoy this meeting between their characters and villains. But they will also search for them; lead their characters to them, and so much more.
Addendum
I also highly recommend reading answers to questions like these two. While they do center on creating a single villain, they are still quite useful and in more than just creating and fleshing each and every one of the villains in the organization.