What is the origin of angular momentum in the early universe? When the univere started to cool down, small differences in density acted as gravitational seeds rigth? then why didn't everything just collapse into those regions. 
What is the origin of the angular momentum that made possible the formation of galaxies and other structures?
 A: Quantities like the total energy, total momentum, and total angular momentum of the universe are not well defined in general relativity. See http://physics.stackexchange.com/questions/2838/total-energy-of-the-universe
It is possible to have an over-all rotation of the universe, but that doesn't convert into an angular momentum, and it pretty strongly violates Newtonian intuition. See http://physics.stackexchange.com/a/12781/4552
Angular momentum is locally conserved in GR. If you have some local region that happens to have zero total angular momentum in the early universe, then the dynamics of that part of the universe can cause, say, half of the region to start spinning one way while the other half spins the other way.
A: The total angular moment of the universe is zero. Locally the AM can be nonzero as in a turbulent medium.
A: The total angular momentum of the universe is considered to be $\vec{L_u} = 0$, but this doesn't prevent certain local areas of the universe from gaining (and losing) angular momentum. Because of the chaotic mechanical formation of the universe, it seems highly plausible that collisions between particles in the early universe created turbulent flows in local region, which evolved into the local angular momenta that we observe.
A: You are right that local density fluctuations were gravitational seeds. And matter nearby that did not have enough energy to overcome the gravitational pull would merge into the object. But if an object had enough velocity in the non radial direction such that merger was not possible but neither escape was, would now start to rotate around the object. 
