I am 80%sure that none of my group uses this fourm. But if you do. And the history section sounds familiar. Stop reading you have been forwarded.

A Little History: I just completed Lost Mines with the Party after a hasty departure from the cave due to the mines caving in, the party was forced to flee. On their way back to Phanalin they were accosted on the road by a group that is specifically hunting down and killing or capturing known heros. They were targeting a specific player character in our group. A wizard who entered into a pact with a demon for more power. He sacrificed his Wizard abilities and became a Warlock. He used to be well known. Said character sacrifices himself and using one if his forbidden abilities to teleport the party to his bolt hole in Neverwinter, and is now presumed dead by the party.

About the Game: I am running a shared campagin with my brother that takes place in Faerun. Both campagins are connected but have completely different objectives and goals. As we both also play in each others campagins we have agreed to only share the most needed information, in order to keep either of us from meta gaming. There is some spoilage of some events that cant be helpped on those such events we step back and let the main party decide. This started when I stepped in to run a game between his sessions and the characters thought it would be cool if they somehow were connected to their other characters and it kind of built from there. The main premise is there is a group of people who want to rewrite history in order to set mankind on the right paths. They plan on doing this by causing so much unbalance and chaos that Lord Ao is forced to step in and wipe the world clean and start over. The group in question has been behind a lot of the more world changing or chaotic happenstance but not directly connected. My brothers group is the one that will be directly hunting down and dealing with the group responsible for it all. While my group piggy backs off of the chaos and has to find means to stop or set to rights some of the things happening. In return they will also be dealing with some of the generals of the group as well as their own back stories and thus weakening or helping foil the plan all together. The general idea is for both parties to come together during the final battle at the end. 

Now the part I need help with: Having used Phandalin as a jumping point they are now in Neverwinter. The cleric who serves Lathander will receive a dream that will pertain a quest to find and seek out the dawnstone, he sees the stone fall into the clutches of a shadow beast with red eyes after shadows covered the stone itself. the party will learn the city has come u Der threat if the same shadow like creatures and they might be connected with one of the lords missing daughters. In turn the Bard will also come across a prophecy that alludes to funding the stone, and a war of blood which is a foreshadow for when the blood war begins to spill more into the material plains and the demons seek to expand their domains of influence. The fey creatures are also starting to reappear in places they used to frequent and wild magic is becoming more frequent due to changes in ley lines. I know I want Velsharoon and Shar to be behind the happenings in Neverwinter, however I am going off rails fir the first time having ran a moduel. I want to create a memorable campagin full of intrigue and twist the party does not see coming but would love advice in how some of you go about planning out your games and sessions. Idealy this campagin would take the characters from 5 to 10 before we would flip back to the other party. 

I think the key to a flexible, believable world is to identify the major players and their agendas and then just have them pursue those agendas. It seems like you have a sequence of events planned out, so think about the consequences of those events and how the world and major players might react to them. If you have several NPCs with agendas and those agendas overlap or conflict with each other at certain points, intrigue is going to be a natural product of that.

Also, listen to your players. I've gotten the inspiration for more than one twist from ideas players have put forward while trying to figure something out. Especially when the idea is quickly discarded, they love it when it turns out to be right in the end after all.

As for running a game in a joint world, I have done that a few times and in my experience sharing information between DMs can have some really cool payoffs. Being able to set plot hooks for each other or otherwise set each other up is a real strength of a shared world, and if you're mature enough to DM you're probably mature enough to not metagame super hard with the information you have. I guess I'm trying to say that you shouldn't minimize your "cross-over" opportunities just because you're afraid of metagaming.

Also, I'd recommend not setting in stone when you shift between campaigns. Another huge benefit of this set up is that you can switch up when you're feeling a bit burnt out. I could never DM full-time, but when my group rotates to me as DM I'm always fresh and ready to go.

Yes. I do have a sequence of events pre-planned in mind. My players are really story driven more than combat driven. So I know that having memorable NPC and dialog will be important. The great side is they give me plenty of story fodder to work for.  

My main thing is funding away to keep track of everything 

There are some published adventures like Rime of the Frostmaiden that have examples of adventure flow-charts for DMs that break the campaign down to more manageable bits. Wild Beyond the Witchlight also has very good examples of printable story tracker sheets for the DM to help keep things organized.