Got it. It was those two pins (front and rear of the block) did not allow the intake to seat properly. I just remove those 2 pins and everything fit at ease.
Since the pins are gone and a large bead of RTV there is recommended, if you'll clean out the holes and use enough RTV to fill the holes this will help anchor the bead. If there is oil or water in that hole when the RTV pushes down into it the oil or water comes out and curupts the seal.