Upgarde Problems 2.0.4

I must have made an error or errors during my installation of 2.0.4 (last upgrade was 2.0). When I click on a file in the publ8ic page I am sent to a Log In page (this has not happened before): http://alplm-cdi.com/chroniclingillinois/files/original/520a9e2739e9312761361ae3b4f1fc02.pdf

When I then log in and go to a file I get a 404 Page Not Found: /chroniclingillinois/files/original/520a9e2739e9312761361ae3b4f1fc02.pdf is not a valid URL.

Also i am unable to index my items and when I tried to use HTML in Item Type Metadata I am just getting html code, not the conversion to text.

How should I go about correcting these errors?

Thank You,

RBM

I was able to address the indexing error and I am now able to convert html code to text in Item Type Metadata, but my other problems are still affecting the site.

Trying to work through this problem. When I go to files/original in my file manager and click on a pdf I get Error 404 - Not Found. Need to find out why the new installation is not picking up my original files.