Did you just simply apply ssl  and then try hitting the site  or did you re-extend shreapoint onto the virtual server? I will need a little more information to help diagnose your problem.

One thing you could try is to delete the website (don't delete the content database, profile, or services databases when you do) through central admin. Then clear out the folder that houses your sharepoint site on the file system (c:\sites\sitename). Apply SSL in IIS. After this, reextend the web  application using SSL during setup.

I looked to see if there was an stsadm.exe way of doing this without unextend-reextend but I did not really see a way (I am sure there is). I know you can apply SSL to the central admin site by doing stsadm.exe -o setadminport -port 9999 -ssl.

Yeah I figured I would just need to recreate the web  app and set  it to
use SSL from the start. We are going to change the root of our url
soon so I will probably wait until then.

Unextending and Re-extending should only take a few minutes to see if
it works. It should not cause any config for content loss either
because thats all on the database side. Hope everything works out well.