I'm going to go out on a limb here, but:
From what I understand, P.W.A.B. was initially organized by the United Nations as a disposal organization meant to clean up what remains of the Gears once the war was over, since they were bioweapons as well as biohazards, especially T-Type Gears. Not just the Gears, however, but anything associated with them, That Man, the various Gear Plants and companies and militaries and countries associated with them. Because of the fact they ignored the means to that end and actually tried to make Gears themselves, as well as facsimiles (the Sentinels, the Kinjuu, Forbidden Magicks), their actions were deemed inhumane and according to Ky, they were supposed to be dismantled.
Meanwhile you've got the history of That Man. Once he successfully completed the first fully manufactured Gear (i.e. the foundation for Justice, note this is NOT the prototype Frederick was), he disappeared from the Gear Project for a number of years. Later on it's assumed that A Country financed him several times over to restart the Gear Project, Frederick retaliated by creating the OutRage and Sacred Treasures. But That Man also worked for a number of countries, Old World Zepp, probably gained some of his data at some point. It is because That Man had his hands in the militaries of the world that multiple Gear Plants even existed.
That said, That Man initially treated his work as a lucrative business, but when things went south and his ideal didn't come to fruition (Gears and humans coexisting, or at the very least, "evolving"), Justice came into the picture. She has any number of possible motivations for doing what she did, pregnancy the least of which. But one key motivation Justice had was, she was made into a weapon, and would have been dismantled if she did anything else but serve as one. It may be that That Man deliberately gave Justice a will (or preserved her original self) for this very purpose, or maybe it was his hope she would be a "Trigger" of sorts, to a better future.
Recall that, That Man, when he was eventually captured by the Gears and held as a prisoner in the main Gear Plant, he laments that he was unable to stop the conflict, what's more he regrets the very notion that mankind would ulimately be the victor of the Crusades, and everything would start over once again (this is prior to I-no's intervention). It wasn't That Man's intention that Mankind be the "sole victor" of the war or for the war to drag out as long as it did. The key to all of this is Dizzy herself. Because the War lasted until 2183, she became involved. Because I-no intervened, the war ended in 2175, a difference of 8 years.
Once I-no altered the world's timeline, she swore allegience to That Man, or at least went along with his plan. This is, I think, where That Man's genuine history actually begins. It is not known how long That Man was an aqaintance of Karasu ("Raven") and the other person. However, things begin to move in a direction That Man finally wanted. Eventually certain aspects of Gear kind have evolved to a state he is satisfied with (I'm sure he's fully aware of Ganymede), and he takes his first steps deeper into the origins of the Prime Fields, namely the source of the Gears, the Backyard. Thus he creates something called The Cube, based on his prototype Primefield data of Sol. I don't know what the Cube was for, but something "created by someone else" wanted it, and sent Valentine to get it.
I can't really say I know for certain if P.W.A.B. is the ones behind Valentine, but it is possible at this point, since they are seeking to obtain data on Dizzy, and have a lot of data on Justice by now. Recall that, in That Man's mind, a Merciless Apocalypse is a type of Forced Change in evolution, but the notion that Valentine is an illegitimate child, denotes she is not worthy to inherit "something".
As for everyone else, we don't know. I'm gonna say a lot can happen in 5-6 years, so you'll have to wait.
Regarding Zappa's outfit: I think it's some kind of safety suit...to prevent him from breaking his bones and such when he wakes up from his episodes...like how people have neck braces after a car accident.
To clarify: Prime Fields are genetic information for a specific kind of Gear, namely a Command Type, like Justice. Though BlazBlue mentions Prime Fields as the names of the Boundary Contact Mediums, they are not the same.