1 - Sometimes I can "force it" if I change the increment levels. Either by changing the depth increment or by changing the stock surface.
I know that's not the clean fix you want, but sometimes I have so much work invested in a mesh that going back to blank page and starting over is like a kick in the stomach.
2 - Often waterline chokes on stuff that works fine with horizontal or vertical too.
3 - If you are using the waterline for roughing you might also try taking silhouettes at your depth increment and using those to perform 2D operations.
4 - If all else fails you can start over making sure to do clean booleans so you have a single watertight structure, and run a "clean" or "Simplify" operation on your source geometry before exporting the STL.
If you are working with an STL created by somebody else there is not telling how much garbage there is inside of it. It might not be salvageable.
1 - Yes I have played the "depth increment" game before and will probably have to this time.
2 - Yep! I plan to finish with a horizontal and that tool pathing looks perfect.
3 - I thought about that but every corner inside and outside has fillets or radii
4 - Yeah I don't know what 75% of that means. I don't think Alibre has a simplify or clean funtion.
5 - It is my own STL made by Alibre. I have removed all internals. Other than the surface I want to machine it is a solid mass.
I'm going to try to play with the levels and see what happens. Thanks