Josie,

1st of all I like your production and overlays of harmonies on this song. With this said after reading all the post above re: pitch and Melodyne I have a different theory, mine is a chord or in my mind anyway a "wrong chord theory".

When the vocal comes to the "Lord is come" line I am hearing a chord that in my mind just does not fit the melody, or after even more thought it could be the style chosen is giving you one too many beats on that chord when they should be a change there.

On a side note regarding "wrong chords" if you have never played with a good trumpet player and experienced the funny face they make (usually followed by a dirty look) when surprised with an incorrect chord or even a variation of the "correct chord" they weren't expecting you haven't lived.

Just my thought, bottom-line very good effort on this old classic.

Later,