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I will be updating both Mushroom Kingdom II and Kongo Jungle Melee tomorrow, Kongo Jungle more so than Mushroom Kingdom II.

I don't know if this helps or not but I tested which Characters' Final Smashes cause glitches on Mushroom Kingdom II:

Mario
Link
Samus & ZSS
Kirby
Fox
Marth
Mr. Game & Watch
Luigi
Zelda/Sheik
Pit
Meta Knight
Falco
Pokemon Trainter
Peach
Yoshi
Ice Climbers
King DeDeDe
Wolf
Lucario
Ness
Toon Link
Olimar
Jigglypuff
Lucas

Donkey Kong's Final Smash causes less glitching than the above characters but its still noticeable.
These characters' Final Smashes cause no glitches:

Pikachu
Diddy Knog
Snake
Ganondorf
Sonic
Bowser
Wario
ROB
Falcon

Also, GigaBowser can sometimes hang off the right-side edge of the lower platform and kill himself.  I can't seem to get him to hang off the left side.  Really not a big deal since he hardly fits there and really deserves to die if he does hang there.

Thanks for the awesome stage(s)!