Ride Height Change Effect Alignment?

All of the above, by differing degrees depending on the nature of your setup.

By lowering it you would increase the amount of flat level camber, and affect the toe in. This is because of the way that toe is affected in mustang steering during compression/jounce (i.e. bump steer). Caster I am not so sure about however it wouldnt surprise me if it was also affected.

In summary, get an alignment after you are happy with the ride height.
 
I have lowered about 10 cars and every one of them has had the camber changed because of the change in ride height. Now I know when the camber changes that affects the other things as well, but the camber is the thing that is affected the most.
That's what my experience has been. Bottom line get an alignment if you like your tires.