With that detail it seems you follow more of a painter's logic than a graphic designer's.
Well I never thought about that, but maybe so.
As far as the layers, not all of them contain parts of the drawing. There's a layer for the original outlines (so I don't lose the original clipping paths) and a layer for the original photo. And there's also a 2nd photo on its own layer. There's a layer that I call "extra stuff" which is paths I might need later and don't want to delete entirely. I make full and elaborate use of layers!
The grapes have 15 layers. The 3 finished grapes share one set of 15. But because the 2 whole grapes lie on top, I just created another set of 15 on an upper set of layers, for those 2. The reason I did that is so I could lock the finished grapes' layers, and not accidentally mess them up. (For me, it's too easy in Inkscape to accidentally drag objects, although that may be more related to my touchpad mouse.) I'll have to unlock those though, when I work on that portion of a grape that's behind the stems. And then finally, the stem has 4 layers, although there may be places where I have to distribute pieces of the stem into certain grape layers (because of how the stem lies on top of some grapes and behind others).
I guess there are a couple of reasons why I use so many layers. One of course is to manage Inkscape's performance issues. (This image is already 1.08 mb!) But I find it really helpful to aid in selection. There are many very small objects, and in certain places there may be 6 or 8 objects overlapping. Even with Alt + click, it can be hard to select the correct object. And also, in the final editing process, I might be editing a lower layer, but I need to switch all the layers back on to see if the edit was correct.
Actually, I submitted a "bug" report about layer visibility being included in the Undo queue and Undo History (long time ago). I could switch a layer on and off 6 or 8 times to make sure 1 single edit looks right (because there are so many subtle areas that can be affected by tweaking a single object) and it's crazy to have those in the Undo History or the undo queue. I think Undo should be for changes on the canvas only. But I guess that's another story.
I actually don't use the Shift + PgUp or PgDn very much, to move objects between layers. I draw the objects on the layer where I want it from the start. Although there are some times when I draw an object without realizing I'm not on the right layer, and then I have to move it. Although I don't find those key shortcuts very hard to use anyway. But I seem to recall that Inkscape has a new layer manager under development, so maybe there's hope for you
Oh no, there will NOT be any more grapes -- those are the hardest part! I'm not sure about the final composition yet. Maybe a thumb and fingers holding the stem, or maybe I will draw some kind of a hook to hold the stem, or maybe some kitchen item could hold the stem, like a coffee cup or something. Wine bottle is a good idea. Actually I've shown a somewhat larger version than 100%....actually the screenshot may be around 200%. Or maybe it will just be the grapes and nothing else?