Using either Stoppers or Vamtimbo's Alt-Futa plug-in with the Custom Merge-loading unabled causes, stages, lighting, music, and props to not load in.
When you setup an alt-futa merge-load for both people in the beginning, it breaks nearly everything if you load a 2 person song (I specifically tried HIMEHINA). If you load a single person scene without alt-futa, then add alt-futa to your person and create an alt-futa merge-load for the next 1 person scene, it only breaks that next loaded scene, but sometimes doesn't for some reason.
It will stay broken even if you reload it w/o merge-load, most scenes will still work fine as long as you don't use merge-load. You have to manually add Alt-futa for each scene.
That Megalink update didn't fix it for me, it actually made it worse, now it's pitch black and I can't get the UI to show up at all after attempting to load a 2 person scene, it also broke everything in 1 person scenes as well, clicking on a song title doesn't respond at all.