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Using Autodesk Fusion 360 or other package to make Lids and other form fitting parts?

First off, thanks for all the great posts and Instructables, I hope to be able to add to the growing collection sometime soon with a few projects I need to document.  

Recently I have been trying to figure out a good way to create form fitting shapes with decent tolerances for  PLA printing.  I am using Autodesk Fusion and Blender using Boolean CGI operations, specifically the  Cut / Difference option. to create a appropriate sized cap. 

If you have a peek at the attached image, the top part (red)  was used as a tool to cut out a matching body from a smaller cylinder (blue).  In the real world If these are printed, the shape would never fit together and if you did, you could never remove them.  

What I would like to do is alter the bottom half to shrink it's surfaces inward about 0.25mm to allow for the expanding of materials.

Every time I've inquired about this on some other forums, the first response Is  'Just use resize' and make the bottom half larger.'  Great idea, but there are a problems. 
  1. The inner plate/cylinder and radius walls expand to be too large
  2. The height changes, leaving a gap between the two surfaces
Any suggestions would be great. I believe there is a path using Differences / Intersect and subtracting that, but I've been failing to find a solution to it. 

I have included the Example top as an STL file. 

Thanks for any suggestions.  And No this is not for a school project. Just a hobbyist looking to understand CAD.

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