In the chancel ('in choir') is where choirs belong. They sound better, they look better, they behave better, they are integrated better, they are focused better and are less distracted. They are where they belong and are more a part of the liturgical action - of what is happening.

As far as the organ is concerned. Settle on a builder while the church is being planned and have him and the architect work together closely on matters of acoustics and design.

Is this for your Ordinariate church?

As most Cathedrals, monastic Chapels, and large churches in England have no apse but a large flat East Wall featuring a large East Window above the altar with a large depiction of something of some Biblical scene perhaps something in the life of the church's saint. Often the window will be flanked by statuary.
You will, of course, want a rood screen and perhaps riddle curtains

The organ should be placed in two facing chambers above the heads of the standing choir.

This is an ordinariate parish, so Mass is celebrated ad orientem at the high altar which is not free-standing. There will indeed probably be a rood screen and riddle curtains.

We have a mixed volunteer choir which currently is around 15 people at full strength. The arrangement we currently use has us in sort of mock stalls (two parallel pews facing the same direction) on the gospel side of the chancel. The organ (which is a toaster but does what we need for the time being) is placed in front of these two pews and is also facing into the chancel (has to be this way because of space). I am both the organist and DM, so the ideal layout will allow me to communicate with the choir while playing.

I am not considering other arrangements for the choir apart from chancel stalls vs. loft. The idea of hiding them behind the altar is certainly interesting, but will not be architecturally possible.

choir stalls (on the sanctuary) are great for singing chant when you have a male (Liturgical) Schola, A choir loft is better if you are going to sing polyphony with a mixed choir.

I agree with this. Our choir is mixed and currently both the men and women vest in cassock and surplice which I have scruples about. I also prefer mixed choirs to be in the gallery. I think the setup we're aiming for currently is to have both a gallery and stalls, and to use one or the other depending on the occasion. This, of course, brings up the question of multiple organ consoles...

Will the stalls be outside or inside the communion rail? The typical Anglican configuration of having the choir stalls to the west of the rail has always perplexed me, and I've wondered if it was really the historic English layout or an Oxford Movement innovation to keep the choir technically outside of the sanctuary and thereby allow female singers. Outside of the Ordinariate, I can't recall ever seeing choir stalls in front of the Communion rail in a Catholic church. The normal location for the rail is near the crossing, not the east end of the sanctuary.

Where I grew up, there were nearly as many Methodist churches as Episcopal ones with a "divided chancel" configuration, but the communion rail in the Methodist churches was invariably on the congregation side of the choir stalls. Back when I did a lot of substitute work, I found the traipsing of the congregation through the chancel for communion somewhat disconcerting in the Episcopal churches. I remember at least one church where the return route took half the congregation through the sacristy.

I've never conducted from the console in a divided chancel configuration, but I know of a number of churches where it's done successfully with well-placed mirrors. I share your reservations about putting women in cassock and surplice. A tunic and cap of the same color as the cassock might be an attractive and complementary possibility if a "vested choir" is insisted upon.

Msgr. Hellriegel's place in some ways was a dream.

As to conducting, I'm much less bothered by chant conducting when the schola is in the front. I don't really enjoy watching someone conduct polyphony etc.

I really like the layout of a parish which I recently visited. It was built in the 1980s IIRC, and for various reasons, they did not build a loft. The organ is on the Epistle side, and they have all of the chairs arranged perpendicular to the altar. You can't see the singers when they are seated, but you can kind of see them if they move forward (they can form a circle or whatever all behind the kneeler/book rack). This church is much wider however, but in any case, the choir is in the front, sort of, but not in a loft, and not behind the rail, so they can have men and women or one or the other, without problems.

If I wanted maximum flexibility and to minimize my scruples, I would arrange it so that the rail does not extend in front of the pews which you use for the choir, but I would build the screen so that you can sort of hide the choir.

I'm not quite sure why some people poo-poo choir lofts; I find them delightful as long as they are large enough. You're high up, out of the way, and it helps with sound projection. If being at the west end is too far, you can take the Covington Cathedral approach and have the large balcony in the transept.

If you can, make sure that there are TWO staircases up to the loft. This can really help with flow, depending on how the church is laid out. If you want to be inclusive, see about having a silent elevator put in. This helps with hauling instruments up, and means that older choir members can still make the ascent. It's a big expense / commitment, but it's worth it in the grand scheme of things. If they put the elevator in a bell tower and connect it to the loft via a little access hallway on the second level, it will be totally unheard in the church.

Have proper choir risers in the loft. As in: built in, and large, deep steps. Have them cast in concrete, if you can, which will help with projection.

I'm a fan of having a movable console if it is feasible (and assuming you don't get a tracker). You don't need it until you reeeeeeally need it.

Make sure the instrument is up a little above the choir. Few things are less pleasant than standing with your head right in front of a facade and having the raw pipe sound blast you 3' from your head. Getting it up also helps protect the pipes from getting dinged.

If you take the split-case design, consider having separate swell controls for the swell shades that open inward, vs. those that open toward the nave. This would allow you to shut the nave shades, and still ride the ones that face in toward the choir, allowing for a modicum of expression whilst still allowing the choir to be better perceived over the organ.

I'm also a big fan of putting greats under expression. If you want to be purist: leave the shades open. But if you do double-expression, then the instrument becomes MUCH more flexible. This is particularly helpful with smaller organs.

If you can have choir stalls / stands installed, all the better. I'm a big fan of the anglican-styled music stands that can hold everyone's music for them in a standing position. This may or may not work for you.

If you can have the space, have access to the choir section from both the middle and the sides. Nothing worse than when someone needs to excuse themselves and a whole row of people has to file out or awkwardly lean out of the way so one person can get in and out.

If you can, see about having the choir room relatively close to the loft (if you get one). Older people cannot robe in the dungeon and then climb 3 flights of stairs to get to the loft to sing and still have energy or breath. If you can, either have the choir room in the basement right beneath the loft and have an elevator (yes, I've seen this before, retrofitted to an older church, no less!), or if the church is built with a larger facade, see about having the choir room in the large central bell tower behind the organ, or in one of the side towers, so you can warm up and then file right out into the loft.

You may also want your office to be closer to the church than the rest of the office building. Maybe. Think about how it would work for you. But if you do have your office in the back of the church, rather than a separate office wing, then you need a dedicated copy machine (yes, copy machine, not a dinky printer) to have at your disposal. You don't want to be running to the other end of the building for prints. In any case, even if your office is elsewhere, having a little work-nook behind the organ, or something like that is still helpful. It's ok to do a little planning during the homily of your fourth mass for the weekend.

Make sure you accommodate for brass or other instrumentalists if you intend to have them. And do not make them sit behind the choir and blast them out.

"I'm not quite sure why some people poo-poo choir lofts; I find them delightful as long as they are large enough. You're high up, out of the way, and it helps with sound projection. If being at the west end is too far, you can take the Covington Cathedral approach and have the large balcony in the transept."

Here's one thing usually overlooked: in older churches, the staircase (usually only one) is often treacherous for choristers with safety issues, who are not always elderly people.

Get video monitors installed. Have a camera in the vestibule, another at the start of the center aisle under the loft, and another of the altar. That way you can see what the heck is going on. Having one in the vestibule is particularly helpful for funerals and weddings.