RJ, a 21st century American one. Thanks for the review, and yes, I am very uncomfortable with the mixture stops: the tenth and twelfth above a third makes my mind reel.

Organ registrations are often unique to the specific instrument. Suggested registrations don't always work in practice.

Franck never played anything the same way twice, or so observers at the time have noted.

It just occurred to me what a thread title looks like to a non-organ player. This first thing that popped into my mind is someone unpacking a bunch of boxes and finding a card reading, "Thank you for your purchase of a Bedient Pipe Organ. Please take a moment to fill out the registration card..."

You have two options: be German Baroque and say nothing about registration or be French baroque and say exactly what you want. Either way you will have the organists guessing....

From the bourbon lands

I say specify the sounds and volumes at the measures you want them
and let the organist sweat the implementation.

I prefer economical and consistent markings especially in the midst of notes,
symbols (+ -) then division (Sw Gt)
then stop family (only use name if particular character desired, e.g., oboe or clarinet)
then length (16 8 4 ...).
My starting shutter indication style (Sw=0%)(Sw<50%)
between manual staff and pedal staff.

Here are PDFs (only because I recently viewed them)
with a variety of marks that suggest answers and inspire layout ...
http://imslp.org/wiki/Organ_Sonata_No.1_(Rogers,_James_Hotchkiss)
http://imslp.org/wiki/Advent_'First_Religious_Suite_for_Organ'_(Yon,_Pietro)

Registration questions.
(1) Chorus reed versus Solo reed or does it matter?
Or does Solo imply the division, i.e., a powerful Reed?
(2) Are you really intending String 8 and String 4 and Solo Reed 8
or are you attempting to optimise the performance,
at certain points (+ Reed - Reed)
rather than alternate (String 8 4) versus (Solo Reed 8)?
(3) How common is a Great Diapason 16?
Do you really desire such gravity?
(4) If you couple the Sw to the Gt with both of similar timbres
and play both hands on Gt
you can grow the Sw registration to full
and finally move the shutters to grow from rumble to roar.

m13
needs voice volume (forte ?)

m45
rest allows registration change
is this where you actually reduce the registration i.e.,
- Solo Reed 8
- Rohrflote 4
or just close the shutters or both?

m64
marking is Swell, but to implement what?

m78
rest allows registration change

m79
marking is [-bracket (A F#) but maybe you really want L-bracket
to indicate the Right Hand takes (D) as a solo
and the left hand takes (D A F#) as accompaniment,
or are you in the process of re-engraving the bass to the pedal staff
and implying "Ped no stops, Sw Ped only".
(I see several stretches of tenths and elevenths, ouch!)
or is the [-bracket a typo?

m94
organ unchanged or is this the point of + Solo Reed 8
or Sw < 100% to support the ff voices

m110-m111
asynchronous ritards ?

m112
rest allows registration change

m115
rest allows registration change

Very helpful eft, thank you. I'm working through your comments.

With regard to coupling: I mostly separated the first few measures because of the voice crossings and duplicated notes, and an intended slight distinction of timbre: if I were to couple Gt and Sw together, even with the hands on different manuals, wouldn't the re-articulations be lost, as the A, for instance, bar 5 - 6, played on both manuals?

I would remove the 16 Diapason in the accompaniment. 16 ft manual stops can and will make your pedal line less clear if the lowest stop the pedal includes is also 16 ft. EFT is correct about the gravity that a 16 Diapason will create. That would be my only suggestion, really, although it does seem like the Sw is used as a solo manual and using strings to support a reed wouldn't be my first choice, although it does work. I would recommend diapasons or flutes to support the reed.

Articulation and crossed voices, okay got it.
Registration at beginning, e.g.,
Sw: Flute 8 4 String 8 4 (to balance Gt)
Gt: Diapason 8 4
Ped: Diapason 16 8 4

Do not need to revoice anything,
for variety it is good to have a manual-stops-only section,
just make clear registration indications,
the lowest notes are played by the feet.
At that point it would be "Ped no stops Sw to Ped only".

As I mentioned above,
specify the sounds you want, at the notes you want them,
the organist can make it work.

Your version two registration plan extracted and condensed ...
m1 = mf = (Gt Diapason 8)(Sw Salicional 8 Celeste 8)
m12 = f = (Gt Diapason 8 4)(Sw Salicional 8 Celeste 8 Flute 4)
m46 = p = (Gt Diapason 8)(Sw Flute 8)
m62 = cresc = (Gt Diapason 16 8)(Sw Salicional 8 Celeste 8 Reed 8)
m78 = f = (Gt Full)
m95 = ff = (Gt Full)

Hmm ... m46 (p) needs different stops to get softer than m1 (mf),
e.g., Left Hand Sw Salicional and Celeste and Right Hand Gt Bourdon.

Concur with Salieri on hearing English organ,
and concur with his above suggestions.

m64-65-66-67-68
You indicate Swell shutters to open gradually
while at same time indicating right foot to play Pedal.
To help organist avoid surprise, put all shutter directions above Ped staff,
m64 write "Sw closed"
and follow it with long greater-sign hairpin (<) extending thru m68

m72 remove Full, spelling Diapason
m78 remove bracket
m94 remove bracket

I have played your second score a few times in the church.
The Diapason used above middle-C is quite pronounced, adding 4' makes it even more.
In my case m1 balance is
(Gt Principal 8) == (Sw Rohr 8 Salicional 8 Celeste 8 Oboe 8, shades open 100%).
Adding on Gt side requires a strong Sw increase
(Gt Prin 8 4) == (Sw Rohr 8 Salicional 8 Celeste 8 Oboe 8 Prin 4 Flute 4).
Pedal Bourdon 16 8 was sufficient.

Feet...operate swell....what? Yeah, you do have to do that and operate foot studs,ventils,etc.

Talk to the server that just came up stairs to tell you that Father is going to add a renewal of vows after the post-communion collect.