First, you need delete file notificationDaemon.js and remove from js/Makefile.am
Second, you need find all code about notificationDaemon, and commented out them.
Then should be work, details please pull code of Deepin Gnome Shell with command:
git clone https://github.com/linuxdeepin/deepin-gnome-shell.git

So deleting notificationDaemon.js and removing the main.js almost seemed to work, except now I don't get any notifications tested via notify-send. Sometimes when I login, notify-osd is running instead of the gnome-shell notifications.... so I'm almost there? Is there an installable package of the deepin version of gnome-shell or are there any certain files I can replace to get notify-osd to work flawlessly without compiling the deepin-gnome-shell?

No, you also need delete notificationDaemon.js from js/Makefile.am and "re-compile" gnome-shell!
Because gnome-shell write those setup in code and compile notification daemon in binary file "gnome-shell", if you don't re-compile gnome-shell, gnome-shell still will use DBus interface "notification.freedestkop.org" that make notify-osd can't work.

Hope above will help you, good luck!

Ah I see! Well, I was able to find the packages for gnome-shell and gnome-shell-common on one of the posts here on the forums. Worked like a charm! NotifyOSD is working and the only problem I had was with overview.js, which I replaced from the gnome-shell version from the ubuntu install.