Debug, Update, and Convert a php based site

A PHP based website need to be brought up to current PHP standards "all code was written in 2003-2004" to make use of new additions to the php library. Some areas of the site have debug error messages that need to be addressed, also a set of member features that need light tweaking. The main layout was done in frames and now needs to be converted to something that would be compatible with explorer, firefox, and chrome with out changing the look of the site. When the site was created all files are in the main directory and would like it to be more structured and categorized also condense down some of the php code to make less pages "example when calling a feature of the site it accesses 3-5 pages of php code" cut it down to 1 or 2 if possible. There is one small issue with the login section kicking people back to login again. I feel its an issue with the cookie session timer