You will need some sort of a session level variable on your server - that is unique to the user. This could be something like pdf_ready (true|false)
You will probably have to trouble at all firing off the AJAX request to start creating the .pdf - You can then allow the user to navigate around. The user will need some sort of a visual cue that their PDF is ready - so you could maintain a small status bar for their "job" - and when the server finishes creating the PDF - it just needs access to the users session level variable. When pdf_ready is true - the UI gets updated and the user can click to claim their freshly minted PDF file. You'll want to track that as well - for cleanup purposes.
ASP has some pretty simple facilities if i remembet - much like JSP and servlets to maintain a user session level variable.
In general you will have to watch out for memory issues as well as a way of cleaning up the PDF files themselves on the server. Session can become bloated if you carry around too much user information in them - and slow down your server - so as a rule you need to use session level data sparingly. Yours is a good case for it though.