re: "I'm told to leave the suspension alone, its great right out of the box. "
There are improvements available- Porsche M030, Porsche ROW M030, Billstein PSS9, etc. Whether to upgrade or not depends on your wallet, your need, SOLO II rules, etc.
re: "I'm also told my base Boxster 5 speed will shift better than the 6 speed S" This is a minority opinion of no relevance to most autocross courses where there are 0-2 shifts involved in the timed section of the course. If you are interested in a shorter shifter throw, B&M makes a popular shifter for the Boxster.
re: "I could not find anyone whom has run an 03 or an 04 Boxster at these events to voice their opinions. Has anyone on this group Autocrossed their Boxster new or old? Any advice?" Take a walk over to the Boxster racing board -
http://www.iq.dynip.com/~racing/index.cgi/index.cgi?
Ad Sach - who might try autocross again if he can find a small enough group.