Hi lee - for the fillets, there does seem to be a misalignment between the pieces, if you zoom in to the top view you can see it:





That will cause a really small edge to be formed there when those pieces are cut with one another and that little tiny edge tends to get in the way of filleting.

It looks like those pieces may have ended up with a slight rotation to them or some kind of deviation from the world axis - if I line up that one area the bottom areas are still not aligned...

I'll see what I can do to patch up that part though, since it looks like it may be a bit difficult to get a full alignment between the existing pieces it is probably easiest to use the "low level" surface/surface filleting mechanism instead of the edge-based filleting. That is a slightly different style of fillet where you do it on 2 individual surfaces that you select it will be able to build the fillet surfaces but then there is some manual trimming to do afterwards.

- Michael