I was in a similar predicament a few months ago. With a 5D3 and a 70-300L, I felt that getting to 400 with a 100-400 was simply too redundant--especially because I love the results I get with my 70-300. I also liked the idea of the 400 f/5.6's lower weight, faster AF and sharper IQ. So, I sprung for the 400 and haven't regretted my purchase one bit. Even with a 1.4X, images are sharp. The AF is very fast. And though it's a bit long in the backpack, it's smaller diameter and lighter weight make for an easy carry. In short, if I had to do it all over again, I would buy these same two lenses.
Footnote: Though I do not own a 100-400, I have borrowed one from a friend of mine on a number of occasions. It's a very nice lens, especially if you only want to carry one. But in concert with my beloved 70-300L, the 400 f/5.6 just made more sense.