For bug limit, say I want to play the first part on 1.2, and the second part on 1.0 (Both North American Wii version). Would this be allowed? I’m asking because for full game runs I would want to, If possible, do the first part on 1.2 so I don’t have to worry about the bugs sinking in Lanayru Twilight. I would want to play the second part in 1.0 because of the Cutscene skip in Cits (When you enter the boss arena. From what I can tell from reading the rules this is allowed.) Would I be able to do this? I would just be taking the disc out and putting the other one in. There would be no save and quit. It would be seamless except for the possibility that it might prompt me to put the disc back in, depending on when I do it.

Update: after some testing, I have found that this may not be possible. I swear I’ve done this before, but it wasn’t working for me. I’ll do some more testing, but for now just ignore this.

No. Same goes for having two setups. Two game discs, two consoles, two capture cards. Even if proof could be provided you must perform the run on the same console and disc you started the run with. This debate came up a few years ago about setting EBF on another setup during the Master Sword cutscene and the like.

To expand on this a bit further: Your idea would not work for bug limit as bug limit is, by definition, no save and quit. The console actually checks the disc you use and while externally (Except to the trained eye which knows where to find the region code), 1.0 and 1.2 are the same, to the console, they are two different games. In order to disc swap you would have to save + reload the game anew, as attempting to hot-swap will cause the console to reject the different version and force the console back to the Wii Menu.

Even if this issue were not an issue for the console, what @SkyreonSkyreon mentioned still holds true - one copy of the game, one console, one disc. In fact, I'd dare say it's probably better to use one controller only, however, I do not believe this has been discussed at length internally.