Summary of workflow:

Complete all machining features in Milling Job 1 and simulate. When I know it's done and I've zoomed in/out on all the areas I want to look at I close Sim and re-open it. At the Medium setting I will hit "x" once or twice to zoom in. Then I regenerate and run the Sim all the way through to the end. Save the STL as Part-Number-OP2-Stock.stl

Create new Milling Job (2). Use STL as stock and complete all machining feature in Milling Job 2. After Simulating many times to make sure it's as I want it, I close it and repeat the steps before: Reload the Sim, hit "x" once or twice, regenerate, run to the end, save as Part-Number-OP3-Stock.stl

Create new Milling Job (3). Use STL as stock just as before but before I even create any more machining features I go back to Milling Job 2 and change the stock to "Rectangular". This will permanently remove the 30-40mb STL from the file, which is more of a common size for me. Rinse, repeat as necessary.

If I need to go back and edit a feature that recognizes stock in Milling Job 2, I will have to run the stock wizard again and re-select the STL but that's just a couple clicks. The key step is NOT moving forward in the stock wizard to the Stock Orientation page. After loading the STL, just hit "OK" to skip that step and it will maintain your origin.