Thank you so much for such a detailed report! Pretty much all of your bug reports have been fixed in the past hour, except for some I deemed way too unnecessary to fix, but about 90% has been done, you'll get credited in the patch notes as a show of graditute! (Unless you specificaly do not want your name mentioned)!
Thank you again for your time and effort of mentioning these mistakes though, must have taken quite some time to write, although, one that I am not a 100% of what you ment is the Photograph not respawning after it gets hit by the shelf. I looked into the code, and nothing indicates this happening, nor did I ever witness it happen, so that is one of the two that I skipped. The other one is the doll getting stuck outside walls, as it is a pretty difficult process to work with physics, but also, it is quite rare for this to happen, as you'd need to specifically INTENTIONALY put objects through walls to make them vanish, and even then, you can simply reload the game, OR use the PC to reset item locations!