[KSky]

The GCode is perfect, the the Z being the top of that part like I want it.

In the simulation, the Z that's shown in the "Move Table" is off by 3.5 inches. Well, it's not really off. I have no tool holder and the Overall Length of the tool (1.5") and the Protrusion Length (2") make up the 3.5 inches. So it seems that the Z in the tool table is the bottom of the spindle nose. Is that right?

How do I set the Overall Length and the Protrusion Length? My 1/8th end mill really only sticks out of the spindle .5 inches.

See the screenshot attached.

[magicniner]

I may have the wrong end of the stick here and this may not be relevant to your problem but how could the protruding length of a tool be greater than it's overall length?
I always set protrusion as the visible (i.e. Protruding - not in the holder) portion of the tool.
Regards,
Nick

[RAF.]

The GCode is perfect, the the Z being the top of that part like I want it.

In the simulation, the Z that's shown in the "Move Table" is off by 3.5 inches. Well, it's not really off. I have no tool holder and the Overall Length of the tool (1.5") and the Protrusion Length (2") make up the 3.5 inches. So it seems that the Z in the tool table is the bottom of the spindle nose. Is that right?

How do I set the Overall Length and the Protrusion Length? My 1/8th end mill really only sticks out of the spindle .5 inches.

See the screenshot attached.

I find that if I set a Flute length at .5 it will auto add .1 so total Protrusion Length would be .6

uncheck system tool and change setting to .5 and see it that works for you.