The metronome mark is wrong/confusing. The mark for compound meter such as 6/8 should be a dotted value, such as dotted quarter. Btw. now when I listen to the song I think that the time signature should be 3/4, or a longer (2 measures) 6/8.
Unfortunately I cannot fix either of those without creating new problems. I can't put in metronome marks and if I copy it to another file in 3/4 I won't be able to remove the abbreviated piano markings like I had someone else do, who is also the person who put in the metronome mark.
Can you or someone else do that?
While what you have sounds amazing (truly), the way it is notated makes it unwieldy for human use. This is not to say the arrangement itself unplayable, but that the accumulation of disorganized layer usage, ambiguity of hand placement, and (here's a biggie) planning triads on 16ths creates serious roadblocks.
I think before you do anything else though, the biggest hurdle that needs to be done is halving all your note durations so that your 6/8 time signature will make sense. Here's what I mean:

See how much cleaner this is? Not only do you see the beat patterns easily, but now all the accompaniment figures all neatly beamed together.
...That's a lot of work. is there some sort of script or quicker way to handle such a conversion?
Also, would changing to 3/4ths avoid that? I'm not sure I'm determined enough to do that if there's no script driven shenanigans to solve that. We're talking like 3-4 hours of clicking every note in the song to make it small and then copy pasting every other measure into the measure before it.
The solution isn't raising the lower notes an octave for measures 5 and 6; the top notes are an octave above the melody so thee lower notes can be played by the right hand. the only reason I never included them there is because I couldn't make clef changes; if I could have I would have separated them from the very beginning.
A lot of these decisions leading to poor notation weren't made by choice really; I've been doing the best I can with what Finale Notepad allows me.