If you've rebooted after the ME upgrade, and ran the Plesk installer again (keeping existing options), and rebooted after *that*, you should have the webmail functioning correctly. It's possible that you installed MailEnable with default options and it didn't bother to try detecting the correct site for webmail.
If that's the case, you may have to login to RDP on the machine, open IIS Admin, drill down to servername > "web sites" > "webmail(mewebmail)" and map the path for the "mewebmail" virtual folder to the correct path (which could be "%plesk%\Mail Servers\Mail Enable\Bin\NETWebMail" or "C:\Inetpub\vhosts\webmail\NETWebMail" or "C:\Program Files\MailEnable\Bin\WebMail" or so on. Find the correct path and map it.