2nd bar of the B section:
1st beat: E-7 (there's a minor 7th in that chord)
2nd beat: it actually sounds like a GM7/D because the strings are holding the G note on top of those four chords, but the rhythm section is actually playing a B-/D. So you can write it either way. But there is definitely no "E" note in that chord.
3rd beat: you can write it as a E-/C, but it's just like a CM7
4th beat: same thing as with the 2nd beat here. There's no "E" note in that chord. It's just a B-7.
1st bar of C section: both chords are minor 7th.
Tempo of the song is 85 or 86, definitely not 90
D9sus chords are the same as A-7/D
Either ways are fine, but with IRP (in general), it's better to use slash chords only when really necessary because of vertical spacing consideration (to avoid overlapping between lines)
I can see most of your points as reasonable; I used the arrangement I had transcribed for my band, mostly because this Delfonics song is not particularly well known
(unlike, for example, the Carpenters' version of "Close to You" which I also did a chart for this weekend); in those instances, I'm like you and try to get as close to the hit recording as possible.
Tempo: Did we play it a little bit faster than the original? Probably, again, I just went with the way my friends and I used to play it.
A few other points, however, might be worth making just for the record:
I noticed that you had the "embellished chords" option checked and I never use that feature because I don't trust irp to do that for me, so I could see why you used straight major chords.
I would take issue with your saying Am7/D is the same as D9sus; yes, of course they are in the real world, but I personally find irp voices those two chords differently; the sus chords always seemed to be voiced in a higher register or inversion.
Your point about about avoiding spacing for slash chords would be reasonable if this was a difficult arrangement with very little space to spare, but it isn't here, obviously.
Good point about Em/C being CM7; I should have noticed that.
You didn't mention anything about my meter changes to get the accented upbeats, so Im going to assume you were OK with that.
Thanks very much for the feedback.