Hi Robert. The problem is in your workflow.

"Boolean" should be reserved for "closed objects", whether they are 2d or 3d. "Join" should be used when needing to join open things, like surfaces.

Here is a video where I zoom in on some fragmented surface pieces that are making your fillets fail. I then rebuild the network with your curves and show you that the "planar" command, will work on any planar openings of an object. You can still select that bottom edge and run planar to create the surface, but then you would use "join", to connect it to the other pieces. Not Boolean.

Also, remember to hide the construction curves from your model. Selecting those, instead of the surface edges, would have the fillet fail also...