I played one note (the last in the seventh measure in the bass clef) as an F natural even though it's not indicated as such. To me, it sounded better this way, but an F natural there also creates a pair of sequential half steps (F# to G and E to F).
If I understand correctly, the square notes (which I tried my best to duplicate in my notation) are chanting tones, but I played them just as regular whole notes.
Because this is a longer tune, I split the notation roughly in half. It was still a bit crowded, so I didn't put an "alternate notes" label for the alternate notes. The small lines above and below the staff at the end of the third line indicate where two sections of alternate notes abut.