1/ Not explained. I seem to recall Vemi and myself thinking of the fluid in the pods as a superenergetic liquid (which is an absurdity of physics; basically imagine they crammed as much energy as possible in without the pods bursting), but the process is thoroughly undefined. I'd say that 'Suifying someone would be a) impossible and b) pointless. Impossible because superenergetic fluid is likely deadly, and pointless because they've perfected cloning. "Resource-intensive" is fairly unimportant for anyone with plothole access. Also bear in mind that these aren't humans/etc we're talking about -- Mary-Sues have glitter for blood.

2/ In our minds, the Mary-Sue Factory was one of the primary sources of 'Sues. In my particular mind, a Mary-Sue is simply a walking nexus of plotholes. Intentionally or not, they manipulate the world around them in profoundly unnatural ways. The Factory must have worked out how to create nexuses (This is all being invented on the fly, here). However, 'brainwashed into servitude' is right out. These are clones and created beings. You don't brainwash them -- you create their minds from scratch (or templates). They can be controlled directly (the Mysterious Somebody did that) but they're not usually an army. It's best to make them annoying and just turn them loose.

3/ Defectives are what the name suggests -- defective. They're the result of the construction process going wrong at some point. The reason they're usually colourless is that a failure at an earlier stage is usually fatal. They're probably slightly less annoying than normal Sues, if only because they're staff -- they need to be people the Flowers can work with, rather than just be irritated by.

4/ The answer to this is the answer to question 3: either a Defective or a dead 'Sue and a quick recycle. In The Reorganisation, the entire original Factory was set to recycle, resulting in every single 'Sue under construction being dissolved. Also, as someone mentioned, if an Agent found a Factory, she'd either be killed or report it to Upstairs, who'd attack in force. Mary-Sue Factories are very bad things.

5/ Probably a combination. They don't need constant supervision, but at least the initial setup is external. They can also be set to recycle at any point. I guess they could probably change anything which isn't initialised yet.

6/ The Factories are essentially miniature versions of HQ. They have Defectives instead of Agents, but there are still Flowers in each one. They aren't robotic places pumping out 'Sues, unless someone wrote something I've not read. They're also covered by Someone Else's Problem fields (or at least the original was).

7/ Nothing. DoSAT could do everything the Factories do if they wanted to, but why bother? Cloning, personality-creation, mixing genetics... they're all canon technologies. Remember the original Factory was actually set up by members of the PPC.

8. Again, 'learn of' is impossible. Every sentient Flower was a former member of the PPC (since the only way they can be created is through a portal set up in HQ), so they already know about World One. It's one world in an infinite Multiverse -- there's nothing particularly worth invading there. Also, to be honest, 'Sues do not work well together. The DTE once let a pair of them kill each other over which was the most beautiful. There have been two armies of 'Sues that I know of -- one under heavy mind-control (during Crashing Down), and one unleashed during the 2008 invasion. That one didn't work as an army, but as a collection of overpowered individuals bent on wreaking havoc.

Also bear in mind that the Flowers of the Factories are doing all this for pretty much two purposes: to afflict the PPC and to gain power/money/etc. The PPC is far better assailed in the way they're currently doing it (eg, Fanfiction.net), and there's not much to be gained from outright invasion.

As to whether individual 'Sues could make a living for themselves in World One -- some would say they already have. :P

hS

PS: Remember that all of the above is only my opinion. I created one Factory; someone else invented the League. The PPC is community property. ~hS

1) I have absolutely no idea, and I believe the answer depends entirely on the author-- hS, I think?

2) Again, what a "normal" Sue is, and what these Sues do, and what the difference is, and if these Sues are following the Words that we can't see... up to their authors, I believe. Personally, I'd long ago begun a story where 'Sues were born/made, in an OFU-style academy. It was a backstory, not an Event, though...

3) No idea. Perhaps if I knew what Defectives were...

4) I thought that'd already been a plot of a story somehow? (Also, wouldn't agents who knew about it, rather than rowdy vandalism, be into a full-on attack?)

5) Again, the author and creator of those pods knows... whoever that is. (I'm almost certain it's hS.) If you'd Permission not only to write Missions, but to use this idea, you'd probably have to ask him.

6 - 8
We write this canon, Max. Asking stuff like this... how can I put it? It's like if you're trying to develop an awesome game in a universe you're helping a handful of people make up, and it's a few years into development, and you keep asking "But what if this character does this? Does this griffin the character rides need food, or does it just graze?" The answer is generally "Look at the guidelines, and then-- what do -you- think?" If you get Permission, a decent beta, and approval, use your own discretion.

That said... It looks like what you're planning is a big-huge-cataclysmic-style Event. I'm fairly sure we've got a ban on those at the moment, in favor of just writing straight-up Missions, because the PPC was becoming some kind of Apocalypto-world. So... yeah. Once you've got Permission, you still need to ask the 'Board to do something like a Sue invasion of World One or what have you. It's... like I said. It's like trying to develop a world, with all these little stories, so most often when you've got little specific questions like "How does this work?" you can just think a bit and ask someone with a little experience to beta your ideas. But when you've got some huge, gigantic, world-shaking idea that's going to involve everyone, will they or no, you've got to -ask-.

Hope at least some of this was helpful. >_>