You're right, this is the heart of the issue. Light may have wanted to give X everything to make him as close to human as possible, but how much he was able to get done is a different question. Especially if you're working from MHX, where Light is already ailing in the middle of the project. I don't like retconning much, so I'm ignoring it, and X1 is less specific -- all we know is he couldn't finish the end of the project.
It would be pretty weird if X was the only one of his kind to have sex organs, wouldn't it? I think I'll compromise and say Light had time to finish X's scalp but not his crotch.
For the record, I keep joking about Light being a pervert because in the Rockman world he's the one who introduces the problem of sex into robotics by building Roll. I don't expect the Classic robots to have any sexual traits, so Light is thinking about the sex of robots even when there's no reason to.