The main link is that earth cult guy who's manipulating the town's secret council. The encounter with the necromancer guy provides the players with a super-obtuse clue (insofar as they can find the mark of the Elder Elemental Eye in his chamber).
I think it's OK, though, for the early adventures to not be overtly part of the main adventure. The idea is just to get the PCs familiar with the area, so they care about it and the people who live there and all that.
I don't understand how the players will figure out that there is a secret council or that the man is part of an earth cult simply by raiding and killing how does this all lead on to the main adventure?
Nyx_Dankana wrote:
Don't worry about them not finding the secret council or the Earth Cult manipulator. You can always drop clues down the line (in the form of letters, maps etc.) that reference back to early quests. So that your players get that moment of, "Oh, that's why all that terribad stuff was happening in Red Larch, the Cult was behind it all along."
And that moment could happen at level 3 or level 10, it'll still be a cool revelation.
I added a map in the treasure of an orc and goblin bandit cave encounter that I created to add to the pre-adventure. The map showed the location of Riverguard Keep and it said that Grimjaw pays for stuff. It also revealed the water cult symbol. Later, when they find the cult priest in the Tomb, and they find the Shallow Grave encounter, they have more than enough leads to keep them going.
Not everything needs to be linked. I think it is more interesting when some encounters are not linked.
For my players (my wife and my daughter), their own exploration is going to lead to the reveal. They've tooled around the valley for a bit, and landed in Feathergale Spire and took part in the Manticore Hunt. Now they're keen on joining the Feathergale Knights, so I'm going to send them on initiation quests that start innocuously enough, but will quickly develop into things that have them at odds with the Council and/or making decisions about killing innocents. I gleefully look forward to things spiralling wildly out of control.
Thanks guys 
I will read all new suggestions
All I did for the Tomb of Moving Stones quest was have the leader, Larrakh, curse the PCs and swear that the "Mountain that Walks" would destory them before he booked it through the secret passage. The players could then make a History/Religion check DC 15 for the story of the Cult of the Black Earth and Ogremoch.
Simple tip- Players absolutely hate enemies getting away. Steering them to hate an enemy is an easy way to get them to buy in to the storyline.