Rank Voicing Issues

I noticed that several ranks have notes with chirps (or squeaks) instead of a chiff. I have since worked through each rank (of version 1.04) and noted the most extreme characteristics. As I am an amateur, some of them are probably fine and it could probably be said that they add to the character of the organ. However, several ranks/notes stick out enough to be distracting.
All of my listening was done with the other sound effects off. Note numbers are based on C4 = middle C and C3 is tenor C.

Principal 16' - Airy
Bourdon 16' - faint squeaks
Quintaton 16' - Jittery
Gambe 8' - Raspy
Voix Celeste 8' - Chirp at C4, Ab5, and E6
Principal 8' - a bit jittery
Flute 8' - Sounds good to me
Flute Traversiere 8' - Airy
Bourdon 8' - Jittery with some chiff squeaks at C4
Prestant 4' - Squeaks at D4, F4, G#4, F#5, A#6
Flute 4' - Squeaks at F4, G#4, C#5
Quint 2-2/3' - Squeaks at F3, D#4, G4
Nasard 2-2/3' - B5 sounds metallic (sticks out)
Doublette 2' - Squeak at D#3
Piccolo 1' - Squeak at D#3
Cornet - Squeaks at G2, D#4, F4, G#4
Plein Jeu III and V - sound good to me
Bombarde 16' - Fundamental missing below G2
Other reeds sound good to me.

p.s. The convention for notating the stop pitch (footage) is to place the (') symbol after the whole number (including the mixed fraction). i.e. Nasard 2 2/3' or 2-2/3' not 2'2/3.