I have a ton of posts up on my GM advise column that cover everything from encounter planning to building a campaign. Check my sig if you're interested.
You're off to a strong start though. You know you want your campaign to be Kalashtar themed, and you have a game world. You'll want to find an area of that world where the Kalashtar are present in numbers.
I don't know much about either the race or the setting, but both seem cool. The Kalasthar are psionic, are they not? That makes psionic themed monsters good bad guys.
I would create a BBEG and make sure you know his or her goals. Then layer on the complexity. Some other powerful beings that serve the BBEG, and then some groups that serve those lieutenants. Then think of a way that the players can get sucked in. Since you are starting at a low level, the PCs likely won't be aware of the BBEG's master strategy, and may not even know he exists. Keep your initial problems small, and let the PCs discover more of the plot as they adventure around.
For example, an Illythid might make a BBEG for a campaign that was going to end at mid-levels, but he'd have to be special.
1) Make him a 15th level psion. That should up his CR.
2) Let him have taken over the mind of a local duke, locking that country in civil war.
3) Say that duke had a secret army of Warforged somewhere. Unleash those on the local population.
4) Let the BBEG be winning the civil war.
5) The BBEG has gotten several powerful allies: A great warrior, a great wizard, and a team of assassins.
6) Make the BBEG work from a secret locale. The PCs will have to find it in order to confront him.
That's just an example of course, but its easy to add on stuff once you have a core idea, which you already do. Have fun!