Like the Poster "Dono" said, you can choose your own characters when you come to live in Japan and register as a temporary citizen. But, you need to be consistent in everything you register. If you register for one thing with a certain kana style, like a bank account, and then change your mind later and register for a credit card account with a different kana, they will NOT be able to link both names. So, you should think carefully and once you choose a combination, you need to stick with it forever (or else, you will face some nasty bureaucracy and problems). Also, you need to consider the easiness of typing that kana combination hundreds of times.
And like the poster above mentioned, there is indeed a strong precedent for ジョアン. I am Portuguese too, but my name is not Joao. You will not be able to transcribe the current Portuguese pronunciation of Joao successfully, I can guarantee that. If you move to Japan and follow this precedent, at least some more Japanese people will be able to remember and write your name, as opposed to you finding a more obscure combination of sounds. Even if you find it cute to create a more complicated combination of kana, this might work against you during your everyday life in Japan. So, once again, consider these things, and if you decide to go against the precedent, be consistent and stick with it until the end.