When I shift into gear everything is fine but when I take it out of either gear it seems like it kills for a little to long and almost stalls. out of the water is fine but in the water it does this. What do you think I should adjust or is this how I am going to live with this???

Being an Alpha drive, you have something that is called an "interupter". When you shift it momentarily kills the motor. It is located were the shift cables are mounted on the starboard side exhaust manifold. This probably needs to be adjusted. I have never done it, but I think it is pretty simple. I'd check a Mercuiser manifold to see how to adjust it.

Check out this on our web site -

http://go-fast.com/mercruiser_alpha_shift_problems.htm

First thing to do is adjust the cables properly. Other than that the most likely thing is a bad shift cable. It has to move very freely otherwise it will put too much pressure on the interrupter switch spring and cause the motor to die. I think you just changed that cable so make sure its not kinked.