2) Between version 1.0, 1.1 and 1.2, which version is recommended? I have been told they are all good for different categories of speed run. I plan on using glitches and doing 100% runs.
1.0 is best for 100%. It only exists for N64, so you would have to play on that for runs. It is possible to inject 1.0 into VC, but that is not allowed for speedrunning.
1) Through VC, I can only get the US version of OoT. I want to begin with the Japanese version, as it seems to be the standard version used for speed runs. I am guessing this is due to the dialogues being shorter, but there might be other considerations. How can I get the Japanese version to run on my Wii?
If your Wii is softmodded, you need to install the WAD of the Japanese version. I think you also need to make it region free.