Hi Laura, I think I can help you out with some of your problems. I've been dealing with the province of Ontario concerning my birth certificate for the past few months, and today is the first time where I actually know what is going on.
Your first step, will be to download the form for an adult change of name, fill it out, and mail it to the office of the registrar general up in Thunder Bay. Pro-tip: Use Xpresspost for mailing your forms if you are concerned about missing birth certificates in the mail, or a long wait.
Step two: You will receive a form in the mail, which you have to sign and send back. The form is merely to state that you are transgendered, and that your change of name will not be published in the Ontario Gazette (I'm not sure if anybody has ever looked at that), for privacy reasons.
Step three: The waiting. As I believe Tom Petty once said, "the waiting is the hardest part".
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My experience with the government has been interesting to say the least, and definitely longer than the eight weeks they said the certificate would take. The government charged my credit card on February 16 for the cost of changing my name, which basically meant that I was approved, and my certificate would be granted. I waited and I waited... and I waited... and I waited... and today I called the office of the registrar general to ask about the status of my new birth certificate. As it turns out, my new name was approved on April 19th, and my new certificate was printed out on the 20th. I'll be receiving it in the mail probably sometime this week.
I hope it doesn't take nearly as long to receive confirmation from the government that I'm now an organ donor.