Organization with threads and folders is key. Without organization, especially with a complex game like GITS, you will quickly forget things and lose data.
Some ideas include:
-Sticky your OOC to your main thread group, as well as the active game thread and any other threads you use all the time.
-Make a common NPC thread. Post a pic and a short description of characters players are likely to encounter frequently. This is a must for PBP, it helps the players acclimate to the game world faster and is great for reference, plus it makes the world seem more real if there is some static ingredients.
-Make an important locations thread. Place down important bits of setting with a picture and description just the way you did with your NPC section. Have both of these threads sticky for quick reference for you and the players. This will also help you get the feel of your world to your players easier.
-Individual thread are a must for each PC, be sure to make them private so players can ask you private questions out of the main threads. Also, I find it useful to use private tags for me only to write in plot hooks and GM data in their threads so that whenever I have an idea for later for a character I have it and it's not spoiled for the player. Then, when I need an idea for their character I peek through their thread and check my notes for a plot hook.
As far as the preparation goes, I recomend that you prepare as much as you are able, then improv. and expect that you will have to improv, and if you don't, you're either forcing your plot on the characters, which will likely make them not have fun since they will have no control of the flow of the story, or, your players are boring and unimaginative. Either answer is the wrong one. To help with this, only write one adventure at a time, and don't write the last 10% of it. Let the PC's do that. Let them figure out how they will save the princess and defeat the big bad. This will make the game more fun for them and for you. As you get more experience you can improv more, and you will have to do it more as well because the world will grow fast if done properly.