The shoe shop is against the street, with a work window and two doors facing outward, and around the corner, there's a regular window and what seems to be a door from the street on the other side. It also has a back door leading to the courtyard where the well is. Directly across from it, we know there's the ofrenda room next to a gate, with a little shade tree that Mama Coco is sitting under at the beginning (probably where Miguel demonsrates his running technique to her, too). Beside the ofrenda room is what looks like a long open dining and kitchen area, which leads to a wall in the middle of the courtyard with a big arch in it. When we see Luisa spreading the petals, you can just see a bit of the shop truck through the arch, so there must be an entrance big enough for vehicles, and we know from the shot of Dante climbing that it's near the truck where you can climb up to Miguel's crawlspace. There's some kind of lower building beside it before you reach the alley. You can also just see part of another outdoor room, and I think it's on that side of the wall-arch that Miguel confronts Elena outside Coco's room. Does this look at least plausible?
Also, I think there may be more rooms behind the ofrenda and dining area. Miguel didn't look like he was going outside when he snuck out of the ofrenda room from the side. There are most likely more rooms beyond what I showed, since this sort of hacienda would be essentially a closed square. Probably the truck comes through a gate.
Also, all those shots? Man, that is a BIG hacienda. I guess there's no business like shoe business.