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Regardless of gender, I would wait on surgery until my child had reached sexual maturity. What they want to be is something they need to have a say in. Yes, it's always difficult to be different, but this isn't that rare: 1 in 2000 live births involve a child with indeterminate genitalia.
Genetic testing and ultrasound can give parents a good idea as to what gender to raise their child, but for me personally that would probably end with whether to call him/her he or she, simply because I would prefer to raise my child in a gender neutral manner regardless.
I'd link you to a great article on the topic in the NYTimes Magazine from a few years ago, but alas, it won't let me. It's titled "What if It's (Sort of) a Boy and (Sort of) a Girl?" by Elizabeth Weil, and features a profile of Cheryl Chase, a well-known intersex activist.
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If I am not better, at least I am different. --Jean-Jacques Rousseau
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