Re: recovery.  I am perfectly okay with a person shifting to recovery and getting the recovery effect.  With two caveats:
1. Their Catch is always in effect.  Always.  Doesn't matter what modular powers they have on at the time they take a wound; if some damage part of the catch, Recovery won't fix it.
2. I wouldn't allow modular to shift into the Mythic level of anything unless you are being very liberal with other pcs and npcs using it.  Even if you allow other pcs to get mythic level abilities, I might think twice about letting modular emulate it.  I think being the absolute best bad*ss should be reserved for the folks who pay 'full price' for it.  But that's just me.

• I want a bunch more skill points than I actually get. Looking up, I didn't even manage to grab any of Alertness, Investigation, Contacts, Guns, or Fists. Probably one of those should replace Steath at Fair.

There is no ideal way in cannon to handle this, but there are a couple of kludges.  Kludge 1: take an aspect like "jack of all trades" or "been around the block" specifically designed to let you use fate points to shore up lower skills.  Kludge 2: take a stunt.  Remember, stunts can be changed between sessions so having one lets you effectively shift around a little bonus on a regular basis. Kludge 3: take Beast Change but rename it something like "broad training" and have it be purely internal. take all your knowledge and social skills in one set, and all your physical skills in another.  In essence, for -1 you double your skill allocations.  It may not be a great fit for your detective but I think this third option works well with spy- or military- type templates, where the character is expected to have a decent, upstanding moral side but be able to switch to killer in a few seconds.  Kludge 4: increase your Conviction and take Guide My Hand.  Link it to your prime concept (protecting the city or whatever).  This lets you use a fate point to substitute Conviction for any skill.  Remember, one of the True Faith wielders in the Dresden Files is an atheist, so nothing says Guide has to have a deity as a source.  Any powerful ideology will do.

• My catch is pure mortals. We're planning on a mob-heavy campaign, so that's probably going to come up pretty often. Is that too broad/too narrow/cheesy/just right/etc for 3 points? Is supernatural toughness a good choice or would a mix of toughness and recovery be better? Maybe just recovery (she's certainly strong enough that she could wear a vest in most situations and her background supports it)?

Personally I'd give you the 4-point catch because its incredibly easy to figure that out on the fly.  The moment Henchmen 1 tears through your defenses, Big Bad observing from the background (or getting the after-action report) knows your weakness. But that's just me.

Maybe the best way to handle the cost is to ask yourself how easy YOU, the player, want it to be to find out your catch.  Remember this is storytelling; for 0, practically nobody in the story will put 2 and 2 together, even if its obvious.  For -1, its probably like an action movie: the story antagonists will be inordinately slow to figure it out, but the smart ones will do so eventually.  For -2, you are making your personal story more realistic, where the bad guys are as smart as the players and figure stuff out after one or two encounters.   Rather than asking what the cost ought to be (based on realism), ask yourself which of those story types do you want your pc to star in? Do you want finding our your catch to be a regular part of your game sessions, something that happens occasionally, or something that never happens?[/list]

Another option: tell the players that you'll go with whatever solution they want - costs nothing, costs FP, costs refresh, whatever - but that they should keep in mind that the bad guys will have the same access they do.  So unless they want every mook in existence coming at them armed with flame wands and enchanted bullet-repelling bracelets, they should think seriously about the 'free' option.

So, now that we are all on the same page, lets get down to brass tacks. We have six swords of metaphysical (and sometimes physical) significance. What awesome things can we do with them?

While it doesn't really fit with the three faith swords, you could go Lord of the Rings on them.  Maybe some evil bad hid a bit of his soul in each, and he wants it back.  Maybe he controls one of them, and through it, has partial control over the rest. To fit this into the DFRPG, you could say one of them has a denarian coin in the hilt.

Or go Dragonbone Chair.  Act 1: face the group with a big outsider bad.  The big bad seems unstoppable for a few sessions.  Act 2: the PC's get wind there's a prophesy about the forces of evil being defeated if they're all brought together.  They work to bring them together. Act 3: somewhere close to the very end let them discover that it's an outsider prophesy, and the "evil" in it is referring to the forces of creation.  So now they've got them together and they have to figure out how to stop the things in motion they started.

Ok... so I've been educating myself about the system and I just picked up the first two books.
2.  Only mortal magic is beholden to the laws of magic, right?  So theoretically, an Emissary of Power could use magic gained from .... The Flying Spaghetti Monster to kill mortals and he/she would not be violating any supernatural laws, right?

As HobbitGuy says, that depends on your group.

But one thing that seems to be common in the dresdenverse is that the other powers who have signed the unseelie accords are pretty lax about enforcing the penalties the White Council enforces on humans.  So one advantage a vampire or sidhe spellcaster should probably have (if you're staying close to the books) is that their bosses are far less likely to care if they kill someone with magic. For example

Sports complex would definitely be a good place, which reminds me: Bars.  Why do a lot of people go to them?  Because they're desperate/lonely/insert negative emotion here.

Not to mention, any big office building would probably be a cesspool of despair and hopelessness. It's not called the "Daily Grind" for nothing.

I'm surprised no one has mentioned casinos, horse tracks, sports betting areas, etc...  If your game is set in Philadelphia, I might be tempted to locate the center of local despair whampire power in Atlantic City, its pretty close.

I'm not sure about it either, but here's one way of thinking about it (please correct me if I'm wrong, I'm a noob about it too):  You choose either 'maneuver' or 'attack,' you don't get both at once.  So, in the first exchange the vamp doesn't get the +2 stress bonus from lasting emotion, because he/she is using a maneuver to establish the emotion and not technically attacking.  In subsequent exchanges he/she can use 'attack' instead and get the bonus.
 

I totally agree with Arctyrix and Wilder that stealing someone's supernatural powers requires the evil people eating.

I guess my issue was that the description of what you have to do (the evil people eating) occurs in the sub-section on supernatural powers; it isn't in the general description of the power.  That's why I asked whether the other two sub-powers had the same requirement, because it seems in the written description to be specific to copying/stealing the supernatural stuff.

Also note I wasn't intending to get "cutting" someone else's skills for free.  The goal was "copying," i.e. they keep their level of ability regardless.   I would have to say that consistency of reading requires that if the evil people eating only applies to the supernatural stuff, the reduction only applies there too.