If I were to attempt a run using a Mii Fighter but with the customs option set to off, would that count for the no customs category?

I think that would be fair, the only other thing i could this to do with Mii Fighters is to use the forms they use in competitive play

So any Mii moveset is allowed to be used in a run only if the customs option is turned off?

There are two options, that one is the first one. And the other one is only allowing the 1111 moveset. But I'm not a mod so I don't know :P

I think i'd allow any mii moveset but no custom power ups or anything if that makes sense

yeah that makes sense ^