I had the same problem with skinny ankles etc. I have fitted heel lifts, tongue pads and c-pads on the ankle bones and I now have very comfortable boots. Essentially all boots are made to fit an average shape - which of us is that? I believe that it is well worth persevering with fitting your own boots as this is something that needs to be done as you ride - one rune/ one fit/ one run/ one fit. I got everything where is felt good over two days or so with velcro dots and then glued it all in place with contact adhesive.
The boots are starting to pack out a little now so I anticipate having to add some more foam.