This is a long thread but within it there are some good suggestions on how to eliminate the slow boot and slow shutdown problem.
I fixed my two Win 8.1 installs by deleting certain drivers that have the problem and updating to drivers that do not have the problem. There are details in this thread as to which drivers are causing the problem.
You can reload and run cleaning programs to no avail. You must get rid of the offending drivers in the Win 8.1 system get the normal fast boot and shutdown times.