First of all, congratulations on getting the Lee Classic Turret. I think you will like it. I do mine.
Here are three VERY useful articles on setting up and using the LCT. They are sequential I, II, III. I found them to be very helpful.
#1
http://www.realguns.com/archives/122.htm" onclick="window.open(this.href);return false;
#2
http://www.realguns.com/archives/123.htm" onclick="window.open(this.href);return false;
#3
http://www.realguns.com/archives/124.htm" onclick="window.open(this.href);return false;
Bookmark them. Print them out. They will help.
Now as for your specific question,
bstach wrote:I have the Lee classic 4 hole turret press, it is mounted and ready to go but as I said before the alignment is off. Here is the problem. Starting off with everything line up, If I pull the handle down the shell holder will come up to the first hole in the turret and will be line up just fine. Now when I start back up with the handle. (This brings the shell holder back down) I go down till I hear the first click and the turret moves. If I stop there and start the down stroke again the shell holder comes back up and everything is still in line. Here is the problem when I stop and the first click the primer holder does not seem to come out enough to set the primer, so I go a little farther to the second click, but if I do that the turret moves just a little more to the right and when you bring the shell holder back up the shell holder and the hole in the turret are not lined up.
I hope I make some kind of sense here. Can anyone help me out? Do I have something set up wrong? Help please

Just to make sure I understand the issue, the primer lever that holds the little cup that receives the new primer from the Safety Prime dispenser does not line up to accept the primer from the Safety Prime dispenser. Is that what you are having a problem with?
For now I am going to assume that that is your problem and try to answer that.
When I got mine I found that the primer lever(and cup) would (sometimes) not fall or open to the correct angle to receive the primer. I solved this by removing the primer lever and buffing the sides and edges of it with a wire brush wheel on my grinder. I polished it up very smooths and gave is a light silicone spray lube. Now it seems to work fine.
Also, I have found that the best time to put the new primer in the cup is right after you have removed the old primer and are just beginning to raise the handle. As you drop the shell holder/shell about one-half inch is puts the little cup in a very good position to accept the new primer.
Generally speaking, make full strokes of the hand lever and the turret will stay aligned with the shell holder. However if you do move the turret a bit, it is easliy corrected by just manually moving it back to the detent.
One other little point, is that on mine the shell holder mover slightly during the four strokes and it is helpful and very easy to push the shellholder back in to position with your thumb if you experience this.
If I have misinterpreted your situation, please restate. But please read the three related articles.