My interests in CS are fairly narrow; I'm mainly interested in numerical analysis and numerical methods for solving differential equations. However, during my undergrad I mainly focused on other, more traditional aspects of CS. I don't have as strong a preparation in the applied math side required for a PhD in Applied Math/Numerical Analysis. A class I took my senior year (second semester!) got me really interested in numerics and I've spent much of my free time since then self-studying the material.
Are there any good CS programs where I can get a good background in applied math/numerical analysis and largely avoid topics like graph theory and combinatorics? With my (relatively) weak preparation in formal math, I think a good math masters is not in the cards.
Many schools offer masters in programs that are not specific to just Cs and math. If you're interest in CS is "fairly narrow" as you described it, I wouldn't look into a masters in CS, I would look into a masters in data computing/statistics or even financial Mathematics. Most of these topics do not require combinatorics and graph theory as pre-reqs or requirements.