Your entire layout absolutely gobsmacks me, as I started out on a very similar course about 4 years ago, but shelved it pro tem, as I became interested in the construction of large and complex narrow gauge locomotives from all ends of the world in 4mm scale.
I have by no means given up on my Haymarket project (which, like yours, involved a cutting down of the main shed to about six two windowed bays) since not only have I accumulated most of the necessary materials, and produced some working drawings, but also I have carved out the necessary extensive set of be-windowed gables in 80 thou styrene sheet, to be laminated with the appropriate Slaters' brickwork.
This was quite hard on the wrists and thumbs.
I don't think my construction techniques will be the same as yours, although it is wonderful to see the ground broken ahead, and to have the opportunity of learning how someone else tackled the challenges. Your initiative to have York Modelmaking cut the windows COULD be a splendid help, although I suspect it comes too late for me, as I believe that I chose to cut to accommodate existing proprietary products which were close to the real thing (but not an exact match).
My reason for posting is that I invested considerable effort in arriving at what I believe to be a reasonably accurate 4mm scale drawing of the externals (both sides, roof plan and east end elevation) of the Haymarket coaling tower. I used all the published photographs I could find, plus those of the very similar tower at Kittybrewster. Although I am no sort of a draftsman, I have spent a fair bit of time over the years in scaling buildings and other artefacts from photographs, and I am confident that the results would more than suffice as the basis of a 4mm scale model. One of the reasons I put this project on hold is that I ran into difficulties of access to the technical drawings (which I hoped would elucidate the internal workings) in the possession of the Scottish National Archive. I managed to obtain the grudging admission of the Director that these are not covered by copyright restrictions which at this date would prohibit access to them, but it seemed that I should have to invest in an eight hundred mile round trip in order to consult them in situ. Basically, I've had other things to do than travel to Edinburgh in order further to argue with civil servants whose salary I help to pay.....
I don't have scanning facilities, but you'd be welcome to a photocopy of the drawings on which you'd have to do some cut-and-stick. The object is a fair size -- my drawing of it came out at over 33 centimetres tall, by about 18 cm by almost 14 cm (the last including the sloping system of rails on which the coal wagons were raised). Although there would be some inaccuracies in the photocopy-cut-and-paste process, you will appreciate that those would be as nothing compared with fudging a model up from a proprietary product, and they would be no greater than those likely to result from whatever construction method you might adopt from scratch.
auldreekie