Re-Aligning a Program

Re-Aligning a Program

I have a program I wrote using a saved alignment, and it also has a manual alignment.
I usually add the manual alignment for the first time I run it then disable it for production.
The program I am currently running was good for our first operation(part on table). Then I needed to check it after we added some side holes, and I need to raise the part 3.08" in the "Z" to be able to check the side holes. I copied the program and I can't seem to modify the program alignment to run production without running the manual alignment every time.
I tried adding an alignment transform, but it keeps changing all the "Z" positions throughout the program. I tried changing the "Z" position in the Leveling Plane but it again changes positions in the program.
I have this issue many times before.
Is there a good way to reposition the part and realign without changing all the "Z" positions?
I have attached the programs.
A nonrelated question, is there an easy way to construct a centerline through a cylinder.
Rich