Yes, legacy collection is perfectly fine since the leaderboard is sorted by in game time, though it'll be less consistent since you can't do the enigma manip. You can read about emulator rules here: https://megamanleaderboards.net/index.php?page=emus And I'd also suggest submitting your runs on this board at mmlb before submitting here: https://megamanleaderboards.net/index.php?game=16
Probably the latter, if another week goes by and the run hasn't been verified yet, you could go and ask on the leaderboard discord. Afaik MMX mods don't right out "reject" runs they just leave them hanging. Here's the link to the discord. https://discord.gg/HEvCjrY
You could use Llanfair, which only requires Java https://github.com/gered/Llanfair/releases As CriscoWild said above you should submit your runs to www.megamanleaderboards.net as this leaderboard is a mirror of that one. If you're playing on console, just record, if you're playing on emulator, here are the guidelines http://www.megamanleaderboards.net/index.php?page=emus although I suggest to only see the accepted emulator list for now. There are many ways to record, most people use OBS Studio https://obsproject.com/
GC version on a backwards compatible Wii is the fastest I think
I'm pretty sure 3DS would be the same as Virtual Console, but the 3DS version in particular is not listed at the moment