Once you start to think a lot about names for your own child, I'd say this kind of thing is pretty common. Something that occurs to me is that namenerds often refer to "naming style", meaning the style of names somebody is attracted to--but it can also refer to issues like these. Some people are "low-stress namers"--they see/hear a name they like, and they run with it. That might mean it's the name their best friend just announced for their baby that suddenly sounds mighty appealing, or the name on the nurse's tag at the hospital. And some people stress/obsess over every quality of a name (that would be me).

I suspect that at least part of your answer will be for your wife to loosen up on some of her exclusionary criteria. Like, a short form of your potential name that is similar to her cousin's daughter's name is almost certainly not a deal breaker. It's the kind of question people bring to the sub a lot, and the opinions tend to be overwhelmingly that it isn't a problem. And for the name that's similar to your sister, it may depend how similar. And how your family's relationship to your sister is. If family ask if your son is named after his aunt, can you say "the similarity is coincidental, but it's nice that they have that connection in how their names sound" or something like that?