Figured it out I think. Took me long enough!
So, here is what I did. Loaded the longest tool. Set it on a 1" gauge block.
Zero the Z
Set the height of the tool as 0
set the rest of the tools from this same position. So all of the tools are referenced from the zero tools 0 Z position
Ref all axis home
Set the edges of the part with an edge finder
Ran the long tool down to 1" gauge block
Set the gauge block height to -1.000, yes duh -1.000, not 1"! Made sense to me once I did not have the tools at weird numbers.
Then, to make a long story short, cut my part successfully

Now, I wrote this all down so I can remember next time. At some point I can see I will need a master tool and will have to assign all my tools to tool numbers and cross that into BobCADCAM somehow, but for now I am just setting the heights each time.....baby steps