A few random comments from looking through it, in order
et in terra pax hominibus: alto G might better stay F#
Rhythm at "voluntatis" anticipates and perhaps spoils the good effect of rhythm at "laudamus te" ... fill in with decoration?
"ctus" of third sanctus, better unision on F than fourth
First "Dei" of agnus dei: it looks kind of cool on the page, but (pardon my intonation hobbyhorse) it just can not be sung: the a minor demands low intonation, and the B major high ... imo that kind of thing even when supported by organ is not good.
Overall, you double every single note of the vocal lines: is that really necessary? Even if they are frequently doubled, a relief might be given to change the accompaniment so that it is clearly supporting (not a counter melody, for example, but notes way out of vocal range) of an easy to sing melodic moment, and there are many of those.
I will move voice II up to the unison in the third 'ctus'.
I do have to confess to being a little unhappy with the accompaniment, and it does seem a bit repetitive to me, and will tweakoneer a bit. (Hopefully I won't tweak too much and wind up with 'too many notes'.)
About the tuning thing: The beginning of the Agnus Dei in really in 'e' minor (despite the appearance to two sharps in the key signature (I might change it to one, and change to two at Agnus III)), does this have any bearing on the intonation; i.e., looks like a [vii - I] progression in 'b'-minor but is really a [iv - V] progression in 'e'.
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