For some reasons, your configuration of IIS was broken. FastCGI handler was installed, but was not enabled in IIS. I have added FastCGI Hanlder restriction (it should be already added by fastcgi installer before).
Starting from 10.3 Plesk site itself switched from ISAPI to FastCGI. This occurred because official support of ISAPI module for PHP 5.3 has been dropped:
http://au2.php.net/manual/en/migration53.windows.php
Support for the ISAPI module has been dropped. Use the improved FastCGI SAPI module instead.
So, after upgrade you have broken Plesk website because of broken configuration of FastCGI. But then, when you have tried to fix the problem, you have changed something in configuration of Plesk website and some virtual directories were dropped.
I have performed the following calls to fix this issue:
cd %plesk_bin%
websrvmng.exe --add-panel-virtual-dir --vdir-name="smb" --physical-path="C:\Program Files\Parallels\Plesk\admin\smb\application\public"
websrvmng.exe --add-panel-virtual-dir --vdir-name="admin" --physical-path="C:\Program Files\Parallels\Plesk\admin\panel\application\public"
websrvmng.exe --add-panel-virtual-dir --vdir-name="skins/branding" --physical-path="C:\Program Files\Parallels\Plesk\var\branding\panel\skins"
websrvmng.exe --add-panel-virtual-dir --vdir-name="sitebuilder" --physical-path="C:\Program Files\Parallels\Plesk\sb\htdocs"
websrvmng.exe --add-panel-virtual-dir --vdir-name="sitebuilder/sites" --physical-path="C:\Program Files\Parallels\Plesk\sb\htdocs\sites"
websrvmng.exe --add-panel-virtual-dir --vdir-name="sitebuilder/skins/branding" --physical-path="C:\Program Files\Parallels\Plesk\var\branding\sb\skins"
Please note, that these commands are internal and provided to you only for information. They can be changed in the following release, you should not rely on them.
Now your Plesk is working.
p.s. As I see, you have some customer sites with PHP enabled as fastcgi. It looks like they were broken too. Now they should be working too. It will be good to understand how you removed FastCGI handler from IIS?
Thank you for feedback. We will fix 2 issues in the following releases:
1) registration of FastCGI handler in IIS
2) add checks for absent virtual directories on Plesk site in reconfigurator.