Frage Used machine with ATC on opposite side - updated screen - now problems

I purchased a used StepCraft V2-600 that had the ATC on the other side of the machine.
I updated the screen and then the ATC was not working because it was on the wrong side.
So I watched the video and changed the tool holder to the correct side.

However, now I have problems. First, I now have to Home the machine, Z first, I move the y over and then home the Y and X.
If I home all, it will hit the tool changer.
Also, when I first tested my changes, it took the first tool. but when I did the second tool, the Z axis crashed into the tool holder.
The last straw for me to stop and write was that when I homed the X and Y axis, the machine location both have positive numbers, it does not change
to zero.
What am I missing? When the machine was reversed, do you thing that some numbers were set that is messing me up?

Thank you.
Harvey

I did not know what to do so I took apart the ATC and placed it on the other side.

However, my problems continue. I kept on troubleshooting but now I'm complete stuck.
I unassembled the tool rest and ran M6t1. It appeared to run correctly.
However, when I ran M6t2 something happens to the z axis. When I first Home the Z axis, the machine location is Zero which is 6 inches above the table.

After I run the M6t2, the z axis machine zero is 3.75 inches above the table.
I thought that the machine location for zero does not change value. (z zero should always be 6 inch if Homed).
I do not know what to do, the z axis keeps going lower into the tool rest.

Thank you,