So what I downloaded, all the notes are playing from 3 MIDI piano tracks called FLEX. I see a bunch of other empty MIDI tracks with guitars and drums and stuff. Is this intended? Are those other tracks leftover from your other version?

It seems pretty fine overall otherwise, but I think the chords are a bit off.

So the progression you have currently in the song is
D, C#m, Bm, A
G, F#m, G, (G#), A

Where it's going sour is that while the Bass is correctly hitting all of the above notes, the chords on top are a bit different:
D, D/C#, Bm, A
G, D/F#, G, E/G#, A

If you adjust the chords to the above, you'll find your chords and melody will mesh a bit better. The C# and G# are both passing tones.
I could be a bit off on those chords, but I have adjusted the notes in question just for the very first part of the song just to compare and contrast linked here.

Nice transcription otherwise though, I like your decision to swing the rhythm, I think that's a nice take on it.

I'll rate 3 stars for now, but I'm game to bump it to 4 or 5 stars.