I have a Joomla Site and a Separate Custom designed section of the site developed in PHP. Joomla has Firboard Forum and hat components and works just fine. Need to integrate user management such that users only need to login once via Joomla, but then also need to capture more information than standard when a user registers for the joomla site. Additional info includes Name, Last Name, username, password, email, User Auth Level, Adress, company, position , department, Active (yes/no field), and a couple of others.
The custom site makes heavy use of session variables to determine if a user is logged in and what his authorization level is, and to send emails on sspecific actions, so these values wouldn have to be passed on.
Alternative is to work with Joomla plugin JFUSION (see [url removed, login to view], especially the Developers area), which allows the Custom section to act as "master" for user management, such that users register and login in custom section and it passes the values on to joomla. This is actually a preferred route as it would leave joomla unchanged and would allow for easy updates, etc, later on.
Please ask if you have specific questions.