MOBS
The Mad Scientist
Are you setting the intake gaskets in place when you check the alignment? You wouldn't think it, but just those thin gaskets still make a big difference in how much it "looks" like it needs removing versus setting gaskets in place. Put a drop of silicone on each side of intake port on heads and use that to hold gaskets straight for ya.
Also, if your heads or block were machined atall, your intake may need it's flange machined also. Check to make sure your ports are lined up when you set the intake on the heads.
Also, if your heads or block were machined atall, your intake may need it's flange machined also. Check to make sure your ports are lined up when you set the intake on the heads.