Hi Jeff, well with my previous comments I was kind of confused about what you were referring to originally since I didn't see anything similar to your screenshots when I opened up your model file.

In those screenshots I just saw what looked like 2 fillet pieces kind of directly overlapping on top of each other in the same space - if one of those fillets was supposed to be cut by the other one in the final model, then instead of using boolean union to do that kind of cutting it could be better to trim the fillet pieces with a curve - I was presuming that you were trying to kind of splice together 2 models that had some overlapping surface area in them? That's what it looked like from your original screenshots anyway.

- Michael