I vote for strategy 2 just by gut but I can't say for sure by your description that I'm positive about what you are trying to do. Can you do a sample file with just a few parts (in BobCAD) so we can get an idea of how you go about it?
What I'm thinking is extruding all your geometry to create a solid, then use a 3D toolpath like Advanced Rough to handle the roughing. You would just need to select the outer circles as boundaries to confine the toolpath to the pockets.
Depending on how fine and accurate your finish needs to be a simple Rest Rough operation could do the finish work. Dirty? Yes. Fast? Yes.