The plot diagram is neat! Thanks for sharing it. I'd be interested to hear more about how you link things together.
Sagiro really stated it best when we were talking about this. His theory is "throw out about five times more plot hooks than you think you need, and see what sticks."
(Hey, my players: no new spoilers in this, but there's some "behind the scenes" stuff that may make me look more like Oscar Zoroaster Phadrig Isaac Norman Henkel Emmannuel Ambroise Diggs and less like the Wizard of Oz. Pay no attention to that man behind the curtain.)
Here's an example. When the campaign started, I had no idea what Strontium's past was. There was no reason to define that yet, of course. Far better to wait, see how the character develops, and look for an opportunity. When the PCs were cleaning out their tower's sub-basement at 5th level and uncovered a possessed book that claimed to be a soul echo of "Nithigol, apprentice of Inquisitor Zacris, Eye of the Crown, Zacris the Undying," I'd just made up the name on the spot. It was too good a name not to use later, though, so I wrote it down. Then I read about how every warforged has a unique head-symbol. What if Strontium had been a possession of Zacris? No, wait, screw that; go big or go home. What if Stron and Zacris were one and the same? So I started to layer the pieces in place. Background on inquisitors and local history, various clues from sages and statues. And now the PC is a huge unknown, a power player whom lots of people fear but who absolutely doesn't have the power to back up his reputation. How that plays out is going to be fascinating; it's the big heavy rock thrown into the still pond, and it will ripple into multiple plot threads.
Same with the execrable Riverlimb family. At the start I knew that Cobalt had supposedly killed a Croghan noble in a bar fight, and that's why he joined the Guard. He thought he'd been framed. What if he hadn't? If not, why was that noble in town? I sure needed someone who was paying for all those lizardman weapons, and the Riverlimbs were a good choice. Okay, but why were they behind this? Were they also behind the attempts to destabilize the PCs' home province of Iskaine? If so, it'd be so that the empire would invade and the province's rich lands would be split up between Croghan and the other neighbors, but that didn't seem right for the Riverlimbs. They seemed pettier than that, as befits a heroic tier villain instead of a paragon tier one. So what was it... okay, I wanted to link it to the raksasha/deva story of Alene/Aleph. I really liked that a lot. Even better, the PCs were still carrying around that wooden sword that they knew was a relic. What if the Riverlimbs wanted a raw source of primal magic to use for some horrible purpose? Bingo! Later, when I knew they were making golems, the rest of the plot links fell into place nicely.
Throw out a ton of plot hooks. See what the players bite at. If you can, work the other ones in around the back side. Defy expectations, look for big cinematic conflicts, and make sure everything makes logical and emotional sense.
