ARe you using appvolumes? That shell load time for me a lot of time is appstacks doing startup, take a look at whats starting with autoruns. I've see apps add things to HKLM\SOFTWARE\Microsoft\Active Setup\Installed Components\
which removing them can help. From the flings site, shell load time is
"Window shell to load, i.e. Explorer. Shell load time starts when we receive a notification from Windows shell load is starting. It ends when the taskbar window is created."
I'm getting around 90 seconds right now, and that's with multiple appstacks. If I pull them off I'm getting around 40 seconds with just UEM enabled. I'm hoping appvolumes 4.0 solves some of this.