The next crazy issue I had was that the auto-set tool that it came with was scripted weird, so I sat here toying with the script trying to get it to work right as it seemed to be running in reverse. Before modifying it, it would search "up" on the Z-Axis for the work surface. I then modified the value in the script to be negative so it would search down, and neglected to realize the other values would then need to be changed too. I went throw a few trial runs that ended in panic as the Z-Axis mashed the end mill down into the pad after finding it twisting the gantry. No damage it seems thankfully.
I finally got fed up, set everything back to the defaults for the script etc and just reversed the motor axis control in Mach 3 and all is working well now. This was great since CamBam seems to want to auto-convert negative and positive values to what it thinks they should be, which was the exact opposite of how the Z axis was running, so I had a hard time trying to understand why I would start a job made with CamBam and it would move UP off the work surface and start milling in mid air! 
Anyways, simply reversing the motor for the Z axis in Mach3 solved all of this.
Next project is actually getting something to mill with a decent look to it, make sure I am not missing steps, etc. I also need to find a better way than using the Heightmap tool in CamBam to get a picture imported for engraving as the heightmap tool in CamBam sucks when you are trying to use a simple Black/White tone bitmap and just want Black to be engraved only.
